Variant rs626758 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000550729.2(KRT128P):n.663+84A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,616 control chromosomes in the GnomAD database, including 7,758 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 0.31 ( 7740 hom., cov: 33)

Exomes 𝑓: 0.31 ( 18 hom. )

Consequence

KRT128P
ENST00000550729.2 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.512

Variant links:

Genes affected

KRT128P (HGNC:48882): (keratin 128, pseudogene)

KRT128P links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRT128P	ENST00000550729.2 linkuse as main transcript	n.663+84A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

47040

AN:

152044

Hom.:

7731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.412

Gnomad AMI

AF:

0.449

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.224

Gnomad SAS

AF:

0.329

Gnomad FIN

AF:

0.298

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.284

GnomAD4 exome

AF:

0.313

AC:

142

AN:

454

Hom.:

AF XY:

0.333

AC XY:

AN XY:

276

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.299

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.309

AC:

47082

AN:

152162

Hom.:

7740

Cov.:

AF XY:

0.311

AC XY:

23107

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.411

Gnomad4 AMR

AF:

0.319

Gnomad4 ASJ

AF:

0.219

Gnomad4 EAS

AF:

0.224

Gnomad4 SAS

AF:

0.329

Gnomad4 FIN

AF:

0.298

Gnomad4 NFE

AF:

0.256

Gnomad4 OTH

AF:

0.285

Alfa

AF:

0.286

Hom.:

763

Bravo

AF:

0.314

Asia WGS

AF:

0.299

AC:

1039

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

4.4

DANN

Benign

0.78

Splicing

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