rs4291477

Variant names:

• chr1-65725392-G-A
• rs4291477
• ENST00000760442.1:n.343-4703C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-65725392-G-A
• chr1-65725392-G-C
• chr1-65725392-G-T

Variant summary

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

The ENST00000760442.1(ENSG00000299098):​n.343-4703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,028 control chromosomes in the GnomAD database, including 17,119 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 0.45 (17119 hom., cov: 32)
• Consequence: ENSG00000299098 ENST00000760442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 8 publications found

Genes affected

ENSG00000299098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299098	ENST00000760442.1	n.343-4703C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67827 AN: 151910 Hom.: 17125 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.476

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.446 AC: 67829 AN: 152028 Hom.: 17119 Cov.: 32 AF XY: 0.449 AC XY: 33397 AN XY: 74304

African (AFR) AF: 0.200 AC: 8314 AN: 41472

American (AMR) AF: 0.483 AC: 7389 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1805 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4161 AN: 5152

South Asian (SAS) AF: 0.451 AC: 2172 AN: 4814

European-Finnish (FIN) AF: 0.573 AC: 6050 AN: 10562

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36442 AN: 67950

Other (OTH) AF: 0.477 AC: 1009 AN: 2114

Alfa AF: 0.507 Hom.: 36504

Bravo AF: 0.430

Asia WGS AF: 0.567 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.78
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4291477; hg19: chr1-66191075; COSMIC: COSV59950954;