3-10983669-A-G

Variant names:

• chr3-10983669-A-G
• rs2930152

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 0.643 in 152,042 control chromosomes in the GnomAD database, including 31,887 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 0.64 (31887 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.816 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: 0.643 AC: 97710 AN: 151924 Hom.: 31839 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.643 AC: 97817 AN: 152042 Hom.: 31887 Cov.: 32 AF XY: 0.648 AC XY: 48158 AN XY: 74328

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.648

Alfa AF: 0.613 Hom.: 15898

Bravo AF: 0.657

Asia WGS AF: 0.798 AC: 2776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2930152; hg19: chr3-11025355;