Variant rs585664 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_175078.3(KRT77):c.965C>T(p.Ser322Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0384 in 1,612,824 control chromosomes in the GnomAD database, including 1,407 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.032 ( 107 hom., cov: 32)

Exomes 𝑓: 0.039 ( 1300 hom. )

Consequence

KRT77
NM_175078.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.63

Variant links:

Genes affected

KRT77 (HGNC:20411): (keratin 77) Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. This gene encodes an epithelial keratin that is expressed in the skin and eccrine sweat glands. The type II keratins are clustered in a region of chromosome 12q13.[provided by RefSeq, Jun 2009]

KRT77 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008925647).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
KRT77	NM_175078.3 linkuse as main transcript	c.965C>T	p.Ser322Phe	missense_variant	5/9	ENST00000341809.8
KRT77	XM_011538288.3 linkuse as main transcript	c.266C>T	p.Ser89Phe	missense_variant	5/9
KRT77	XM_011538289.3 linkuse as main transcript	c.*122C>T		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
KRT77	ENST00000341809.8 linkuse as main transcript	c.965C>T	p.Ser322Phe	missense_variant	5/9	1	NM_175078.3	P1
KRT77	ENST00000553168.1 linkuse as main transcript	c.*303C>T		3_prime_UTR_variant, NMD_transcript_variant	6/10	1
	ENST00000547533.1 linkuse as main transcript	n.351+1075G>A		intron_variant, non_coding_transcript_variant		3
KRT77	ENST00000550823.1 linkuse as main transcript	n.612C>T		non_coding_transcript_exon_variant	1/2	5

Frequencies

GnomAD3 genomes

AF:

0.0318

AC:

4835

AN:

152170

Hom.:

107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0175

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0277

Gnomad ASJ

AF:

0.0268

Gnomad EAS

AF:

0.00713

Gnomad SAS

AF:

0.0726

Gnomad FIN

AF:

0.0383

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0398

Gnomad OTH

AF:

0.0359

GnomAD3 exomes

AF:

0.0359

AC:

9021

AN:

251228

Hom.:

212

AF XY:

0.0385

AC XY:

5225

AN XY:

135764

show subpopulations

Gnomad AFR exome

AF:

0.0158

Gnomad AMR exome

AF:

0.0176

Gnomad ASJ exome

AF:

0.0302

Gnomad EAS exome

AF:

0.00783

Gnomad SAS exome

AF:

0.0680

Gnomad FIN exome

AF:

0.0418

Gnomad NFE exome

AF:

0.0395

Gnomad OTH exome

AF:

0.0388

GnomAD4 exome

AF:

0.0390

AC:

57024

AN:

1460536

Hom.:

1300

Cov.:

AF XY:

0.0403

AC XY:

29248

AN XY:

726310

show subpopulations

Gnomad4 AFR exome

AF:

0.0162

Gnomad4 AMR exome

AF:

0.0187

Gnomad4 ASJ exome

AF:

0.0286

Gnomad4 EAS exome

AF:

0.00724

Gnomad4 SAS exome

AF:

0.0685

Gnomad4 FIN exome

AF:

0.0417

Gnomad4 NFE exome

AF:

0.0396

Gnomad4 OTH exome

AF:

0.0361

GnomAD4 genome

AF:

0.0317

AC:

4835

AN:

152288

Hom.:

107

Cov.:

AF XY:

0.0331

AC XY:

2461

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0174

Gnomad4 AMR

AF:

0.0277

Gnomad4 ASJ

AF:

0.0268

Gnomad4 EAS

AF:

0.00715

Gnomad4 SAS

AF:

0.0735

Gnomad4 FIN

AF:

0.0383

Gnomad4 NFE

AF:

0.0398

Gnomad4 OTH

AF:

0.0360

Alfa

AF:

0.0371

Hom.:

150

Bravo

AF:

0.0278

TwinsUK

AF:

0.0356

AC:

132

ALSPAC

AF:

0.0449

AC:

173

ESP6500AA

AF:

0.0163

AC:

ESP6500EA

AF:

0.0399

AC:

343

ExAC

AF:

0.0364

AC:

4421

Asia WGS

AF:

0.0340

AC:

117

AN:

3478

EpiCase

AF:

0.0395

EpiControl

AF:

0.0406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.55

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.12

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.51

Eigen

Pathogenic

0.82

Eigen_PC

Pathogenic

0.69

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.86

MetaRNN

Benign

0.0089

MetaSVM

Uncertain

0.58

MutationAssessor

Pathogenic

4.1

MutationTaster

Benign

0.86

D;D

PrimateAI

Uncertain

0.52

PROVEAN

Pathogenic

-5.9

REVEL

Uncertain

0.50

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.17

MPC

0.78

ClinPred

0.086

GERP RS

4.8

Varity_R

0.91

gMVP

0.32

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over