rs4631830

chr10-46052478-A-G

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 0.432 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.445

Alfa AF: 0.426 Hom.: 11636

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4631830; hg19: chr10-51543344;