6-32606394-G-C

Variant names:

• chr6-32606394-G-C
• rs615672

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 0.416 in 151,796 control chromosomes in the GnomAD database, including 13,723 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 0.42 (13723 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 77 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 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: 0.416 AC: 63089 AN: 151678 Hom.: 13710 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.416 AC: 63148 AN: 151796 Hom.: 13723 Cov.: 31 AF XY: 0.416 AC XY: 30907 AN XY: 74208

African (AFR) AF: 0.510 AC: 21066 AN: 41322

American (AMR) AF: 0.391 AC: 5956 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1300 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3092 AN: 5152

South Asian (SAS) AF: 0.411 AC: 1977 AN: 4814

European-Finnish (FIN) AF: 0.373 AC: 3942 AN: 10562

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24528 AN: 67910

Other (OTH) AF: 0.426 AC: 897 AN: 2106

Alfa AF: 0.393 Hom.: 1456

Bravo AF: 0.421

Asia WGS AF: 0.471 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.75
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs615672; hg19: chr6-32574171;