6-30076611-G-C

Variant names:

• chr6-30076611-G-C
• rs3132682

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 0.611 in 151,932 control chromosomes in the GnomAD database, including 28,582 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 0.61 (28582 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92664 AN: 151814 Hom.: 28533 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.611 AC: 92769 AN: 151932 Hom.: 28582 Cov.: 31 AF XY: 0.608 AC XY: 45129 AN XY: 74210

African (AFR) AF: 0.665 AC: 27554 AN: 41420

American (AMR) AF: 0.653 AC: 9976 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2313 AN: 3472

East Asian (EAS) AF: 0.515 AC: 2656 AN: 5162

South Asian (SAS) AF: 0.627 AC: 3020 AN: 4818

European-Finnish (FIN) AF: 0.530 AC: 5589 AN: 10536

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39533 AN: 67932

Other (OTH) AF: 0.635 AC: 1339 AN: 2110

Alfa AF: 0.595 Hom.: 14930

Bravo AF: 0.624

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.9
DANN	Benign	0.89
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs3132682; hg19: chr6-30044388;