rs3130609

Variant names:

• chr6-33021744-C-T
• rs3130609

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 0.0523 in 152,232 control chromosomes in the GnomAD database, including 289 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 0.052 (289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0523 AC: 7954 AN: 152114 Hom.: 288 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0465

Gnomad ASJ AF: 0.0694

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0523 AC: 7965 AN: 152232 Hom.: 289 Cov.: 33 AF XY: 0.0496 AC XY: 3691 AN XY: 74436

African (AFR) AF: 0.105 AC: 4379 AN: 41524

American (AMR) AF: 0.0463 AC: 709 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0694 AC: 241 AN: 3472

East Asian (EAS) AF: 0.0365 AC: 189 AN: 5184

South Asian (SAS) AF: 0.0340 AC: 164 AN: 4824

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10610

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0304 AC: 2065 AN: 68004

Other (OTH) AF: 0.0725 AC: 153 AN: 2110

Alfa AF: 0.0357 Hom.: 193

Bravo AF: 0.0589

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.0
DANN	Benign	0.78
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs3130609; hg19: chr6-32989521;