rs4291477

chr1-65725392-G-Achr1-65725392-G-Cchr1-65725392-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;