rs3130299

Variant names:

• chr6-32235760-A-G
• rs3130299

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 0.246 in 151,944 control chromosomes in the GnomAD database, including 4,994 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 0.25 (4994 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37322 AN: 151826 Hom.: 4993 Cov.: 30

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.246 AC: 37353 AN: 151944 Hom.: 4994 Cov.: 30 AF XY: 0.244 AC XY: 18137 AN XY: 74282

African (AFR) AF: 0.188 AC: 7773 AN: 41426

American (AMR) AF: 0.343 AC: 5232 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1798 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1415 AN: 5172

South Asian (SAS) AF: 0.241 AC: 1161 AN: 4822

European-Finnish (FIN) AF: 0.166 AC: 1748 AN: 10550

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17280 AN: 67940

Other (OTH) AF: 0.281 AC: 593 AN: 2108

Alfa AF: 0.253 Hom.: 19955

Bravo AF: 0.255

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.15
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3130299;

hg19: chr6-32203537;