Variant chr12-52360731-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_002283.4(KRT85):c.*122A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 1,183,240 control chromosomes in the GnomAD database, including 164,173 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 22419 hom., cov: 33)

Exomes 𝑓: 0.52 ( 141754 hom. )

Consequence

KRT85
NM_002283.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.470

Variant links:

Genes affected

KRT85 (HGNC:6462): (keratin 85) The protein encoded by this gene is a member of the keratin gene family. As a type II hair keratin, it is a basic protein which heterodimerizes with type I keratins to form hair and nails. The type II hair keratins are clustered in a region of chromosome 12q13 and are grouped into two distinct subfamilies based on structure similarity. One subfamily, consisting of KRTHB1, KRTHB3, and KRTHB6, is highly related. The other less-related subfamily includes KRTHB2, KRTHB4, and KRTHB5. [provided by RefSeq, Jul 2008]

KRT85 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 12-52360731-T-C is Benign according to our data. Variant chr12-52360731-T-C is described in ClinVar as [Benign]. Clinvar id is 1280746.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRT85	NM_002283.4 linkuse as main transcript	c.*122A>G		3_prime_UTR_variant	9/9	ENST00000257901.7	NP_002274.1
KRT85	NM_001300810.1 linkuse as main transcript	c.*122A>G		3_prime_UTR_variant	7/7		NP_001287739.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRT85	ENST00000257901.7 linkuse as main transcript	c.*122A>G		3_prime_UTR_variant	9/9	1	NM_002283.4	ENSP00000257901	P1
KRT85	ENST00000544265.1 linkuse as main transcript	c.*122A>G		3_prime_UTR_variant	7/7	2		ENSP00000440240

Frequencies

GnomAD3 genomes

AF:

0.539

AC:

81829

AN:

151868

Hom.:

22389

Cov.:

show subpopulations

Gnomad AFR

AF:

0.626

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.402

Gnomad EAS

AF:

0.632

Gnomad SAS

AF:

0.579

Gnomad FIN

AF:

0.484

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.503

Gnomad OTH

AF:

0.509

GnomAD4 exome

AF:

0.522

AC:

538826

AN:

1031254

Hom.:

141754

Cov.:

AF XY:

0.524

AC XY:

277573

AN XY:

529748

show subpopulations

Gnomad4 AFR exome

AF:

0.631

Gnomad4 AMR exome

AF:

0.509

Gnomad4 ASJ exome

AF:

0.413

Gnomad4 EAS exome

AF:

0.634

Gnomad4 SAS exome

AF:

0.587

Gnomad4 FIN exome

AF:

0.490

Gnomad4 NFE exome

AF:

0.512

Gnomad4 OTH exome

AF:

0.526

GnomAD4 genome

AF:

0.539

AC:

81903

AN:

151986

Hom.:

22419

Cov.:

AF XY:

0.538

AC XY:

39979

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.626

Gnomad4 AMR

AF:

0.493

Gnomad4 ASJ

AF:

0.402

Gnomad4 EAS

AF:

0.633

Gnomad4 SAS

AF:

0.581

Gnomad4 FIN

AF:

0.484

Gnomad4 NFE

AF:

0.503

Gnomad4 OTH

AF:

0.509

Alfa

AF:

0.518

Hom.:

4616

Bravo

AF:

0.545

Asia WGS

AF:

0.596

AC:

2074

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over