rs4460629

Variant names:

• chr1-155162859-T-C
• rs4460629

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 0.558 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.527

Alfa AF: 0.488 Hom.: 24188

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4460629; hg19: chr1-155135335;