rs4747796

Variant names:

• chr10-8514192-G-A
• rs4747796
• ENST00000451609.1:n.915C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-8514192-G-A
• chr10-8514192-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451609.1(KRT8P37):​n.915C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 747,432 control chromosomes in the GnomAD database, including 77,504 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 0.44 (14776 hom., cov: 32)
  • Exomes 𝑓: 0.45 (62728 hom.)
• Consequence: KRT8P37 ENST00000451609.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 1 publications found

Genes affected

KRT8P37 (HGNC:39871): (keratin 8 pseudogene 37)

ENSG00000304440 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRT8P37		n.8514192G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRT8P37	ENST00000451609.1	n.915C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000304440	ENST00000803407.1	n.257C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66166 AN: 151998 Hom.: 14773 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.442

GnomAD4 exome AF: 0.454 AC: 270262 AN: 595314 Hom.: 62728 Cov.: 5 AF XY: 0.453 AC XY: 146247 AN XY: 322916

African (AFR) AF: 0.334 AC: 5561 AN: 16666

American (AMR) AF: 0.465 AC: 17404 AN: 37400

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 8981 AN: 19784

East Asian (EAS) AF: 0.294 AC: 9979 AN: 33924

South Asian (SAS) AF: 0.398 AC: 26293 AN: 66142

European-Finnish (FIN) AF: 0.479 AC: 21855 AN: 45608

Middle Eastern (MID) AF: 0.484 AC: 1189 AN: 2458

European-Non Finnish (NFE) AF: 0.482 AC: 164705 AN: 341686

Other (OTH) AF: 0.452 AC: 14295 AN: 31646

GnomAD4 genome AF: 0.435 AC: 66174 AN: 152118 Hom.: 14776 Cov.: 32 AF XY: 0.434 AC XY: 32285 AN XY: 74354

African (AFR) AF: 0.337 AC: 14011 AN: 41516

American (AMR) AF: 0.473 AC: 7227 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1562 AN: 3466

East Asian (EAS) AF: 0.327 AC: 1686 AN: 5152

South Asian (SAS) AF: 0.390 AC: 1878 AN: 4814

European-Finnish (FIN) AF: 0.472 AC: 4998 AN: 10580

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33367 AN: 67988

Other (OTH) AF: 0.437 AC: 923 AN: 2110

Alfa AF: 0.458 Hom.: 2015

Bravo AF: 0.434

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4747796; hg19: chr10-8556155;