rs6804331

chr3-104035543-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;