rs4291477

Variant names:

• chr1-65725392-G-A
• rs4291477

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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.477

Alfa AF: 0.514 Hom.: 27685

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

Splicing

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

Publications

LitVar

Other links and lift over

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