rs3131854

chr6-29644108-T-Cchr6-29644108-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 0.783 in 152,156 control chromosomes in the GnomAD database, including 46,850 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 0.78 (46850 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

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 (EAS) allele frequency at 95% confidence interval = 0.829 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: 0.783 AC: 119071 AN: 152038 Hom.: 46808 Cov.: 33

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.783 AC: 119170 AN: 152156 Hom.: 46850 Cov.: 33 AF XY: 0.780 AC XY: 58036 AN XY: 74390

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.782

Alfa AF: 0.793 Hom.: 68282

Bravo AF: 0.796

Asia WGS AF: 0.827 AC: 2879 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	0.19
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3131854; hg19: chr6-29611885;