rs3903160

chr6-29965120-G-Achr6-29965120-G-C

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 0.274 in 144,618 control chromosomes in the GnomAD database, including 5,528 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 0.27 (5528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 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: 0.274 AC: 39662 AN: 144524 Hom.: 5524 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.274 AC: 39675 AN: 144618 Hom.: 5528 Cov.: 32 AF XY: 0.275 AC XY: 19389 AN XY: 70536

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.256

Alfa AF: 0.286 Hom.: 3667

Bravo AF: 0.255

Asia WGS AF: 0.197 AC: 679 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.7
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3903160; hg19: chr6-29932897;