3-10983669-A-G

Position:

• chr3-10983669-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 0.643 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;