3-138934646-A-G

Variant names:

• chr3-138934646-A-G
• rs10804661

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 0.184 in 152,080 control chromosomes in the GnomAD database, including 4,187 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 0.18 (4187 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.592 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: 0.184 AC: 27974 AN: 151962 Hom.: 4169 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.184 AC: 28029 AN: 152080 Hom.: 4187 Cov.: 33 AF XY: 0.190 AC XY: 14088 AN XY: 74330

African (AFR) AF: 0.348 AC: 14425 AN: 41450

American (AMR) AF: 0.102 AC: 1562 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3470

East Asian (EAS) AF: 0.610 AC: 3137 AN: 5140

South Asian (SAS) AF: 0.126 AC: 607 AN: 4830

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10586

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0789 AC: 5361 AN: 67984

Other (OTH) AF: 0.158 AC: 335 AN: 2114

Alfa AF: 0.112 Hom.: 5055

Bravo AF: 0.188

Asia WGS AF: 0.374 AC: 1303 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	0.74
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10804661; hg19: chr3-138653488;