rs4929810

Variant names:

• chr10-123990604-A-G
• rs4929810

Your query was ambiguous. Multiple possible variants found:

• chr10-123990604-A-G
• chr10-123990604-A-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 0.745 in 152,144 control chromosomes in the GnomAD database, including 42,392 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 0.74 (42392 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.77 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: 0.745 AC: 113259 AN: 152026 Hom.: 42363 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.745 AC: 113336 AN: 152144 Hom.: 42392 Cov.: 33 AF XY: 0.741 AC XY: 55140 AN XY: 74372

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.753

Alfa AF: 0.767 Hom.: 72429

Bravo AF: 0.749

Asia WGS AF: 0.611 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4929810; hg19: chr10-125750120;