rs10804661

Variant names:

• chr3-138934646-A-G
• rs10804661

Your query was ambiguous. Multiple possible variants found:

• chr3-138934646-A-G
• chr3-138934646-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 0.184 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.0789

Gnomad4 OTH AF: 0.158

Alfa AF: 0.0963 Hom.: 2304

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10804661; hg19: chr3-138653488;