rs2691678

chr3-41188832-A-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 0.192 in 152,162 control chromosomes in the GnomAD database, including 3,646 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 0.19 (3646 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 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: 0.192 AC: 29154 AN: 152044 Hom.: 3643 Cov.: 31

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.192 AC: 29146 AN: 152162 Hom.: 3646 Cov.: 31 AF XY: 0.192 AC XY: 14309 AN XY: 74392

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.218

Alfa AF: 0.234 Hom.: 2071

Bravo AF: 0.175

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.2
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2691678; hg19: chr3-41230323;