rs4460629

Variant names:

• chr1-155162859-T-C
• rs4460629

Variant summary

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

The variant allele was found at a frequency of 0.558 in 152,002 control chromosomes in the GnomAD database, including 24,330 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 0.56 (24330 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 38 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.557 AC: 84674 AN: 151884 Hom.: 24286 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.558 AC: 84764 AN: 152002 Hom.: 24330 Cov.: 31 AF XY: 0.559 AC XY: 41532 AN XY: 74306

African (AFR) AF: 0.670 AC: 27764 AN: 41428

American (AMR) AF: 0.598 AC: 9126 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1412 AN: 3470

East Asian (EAS) AF: 0.803 AC: 4147 AN: 5162

South Asian (SAS) AF: 0.528 AC: 2545 AN: 4820

European-Finnish (FIN) AF: 0.526 AC: 5560 AN: 10562

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32523 AN: 67980

Other (OTH) AF: 0.527 AC: 1110 AN: 2106

Alfa AF: 0.497 Hom.: 31366

Bravo AF: 0.573

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.8
DANN	Benign	0.88
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs4460629; hg19: chr1-155135335;