chr3-39708102-A-G

Variant names:

• chr3-39708102-A-G
• rs9832461

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 0.261 in 152,164 control chromosomes in the GnomAD database, including 5,506 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 0.26 (5506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 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: 0.260 AC: 39596 AN: 152046 Hom.: 5484 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.261 AC: 39652 AN: 152164 Hom.: 5506 Cov.: 32 AF XY: 0.256 AC XY: 19060 AN XY: 74404

African (AFR) AF: 0.362 AC: 15003 AN: 41486

American (AMR) AF: 0.215 AC: 3282 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3470

East Asian (EAS) AF: 0.126 AC: 653 AN: 5182

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4826

European-Finnish (FIN) AF: 0.200 AC: 2118 AN: 10594

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16100 AN: 67998

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.240 Hom.: 14005

Bravo AF: 0.261

Asia WGS AF: 0.175 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.36
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs9832461; hg19: chr3-39749593;