rs6804331

Variant names:

• chr3-104035543-T-G
• rs6804331

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 0.354 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.256 AC: 10633 AN: 41496

American (AMR) AF: 0.364 AC: 5561 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1714 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1958 AN: 5160

South Asian (SAS) AF: 0.266 AC: 1283 AN: 4820

European-Finnish (FIN) AF: 0.309 AC: 3260 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28076 AN: 67958

Other (OTH) AF: 0.381 AC: 805 AN: 2112

Alfa AF: 0.403 Hom.: 20840

Bravo AF: 0.359

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.23
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6804331; hg19: chr3-103754387;