rs6804331

Variant names:

• chr3-104035543-T-G
• rs6804331

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 0.354 in 152,056 control chromosomes in the GnomAD database, including 10,028 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 0.35 (10028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.355 AC: 53868 AN: 151938 Hom.: 10033 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.354 AC: 53866 AN: 152056 Hom.: 10028 Cov.: 32 AF XY: 0.350 AC XY: 25968 AN XY: 74298

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.381

Alfa AF: 0.407 Hom.: 16753

Bravo AF: 0.359

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6804331; hg19: chr3-103754387;