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 ENST00000803407.1(ENSG00000304440):​n.257C>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: ENSG00000304440 ENST00000803407.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803407.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRT8P37	ENST00000451609.1	TSL:6	n.915C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000304440	ENST00000803407.1		n.257C>T		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4747796;

hg19: chr10-8556155;