rs4631830

Variant names:

• chr10-46052478-A-G
• rs4631830

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 0.432 in 152,114 control chromosomes in the GnomAD database, including 14,318 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 0.43 (14318 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 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: 0.432 AC: 65598 AN: 151994 Hom.: 14301 Cov.: 33

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.432 AC: 65654 AN: 152114 Hom.: 14318 Cov.: 33 AF XY: 0.432 AC XY: 32116 AN XY: 74376

African (AFR) AF: 0.464 AC: 19261 AN: 41470

American (AMR) AF: 0.399 AC: 6095 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1668 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2359 AN: 5180

South Asian (SAS) AF: 0.522 AC: 2518 AN: 4826

European-Finnish (FIN) AF: 0.342 AC: 3621 AN: 10588

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28573 AN: 67996

Other (OTH) AF: 0.445 AC: 937 AN: 2106

Alfa AF: 0.424 Hom.: 34951

Bravo AF: 0.431

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.54
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs4631830; hg19: chr10-51543344;