chr6-7649999-C-A

Variant names:

• chr6-7649999-C-A
• rs2327017

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 0.597 in 152,080 control chromosomes in the GnomAD database, including 28,552 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 0.60 (28552 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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: 0.597 AC: 90652 AN: 151962 Hom.: 28528 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.597 AC: 90727 AN: 152080 Hom.: 28552 Cov.: 32 AF XY: 0.598 AC XY: 44461 AN XY: 74340

African (AFR) AF: 0.378 AC: 15678 AN: 41460

American (AMR) AF: 0.706 AC: 10792 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2528 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3720 AN: 5168

South Asian (SAS) AF: 0.594 AC: 2859 AN: 4816

European-Finnish (FIN) AF: 0.663 AC: 7010 AN: 10566

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.673 AC: 45789 AN: 67994

Other (OTH) AF: 0.675 AC: 1425 AN: 2112

Alfa AF: 0.645 Hom.: 17065

Bravo AF: 0.593

Asia WGS AF: 0.672 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.57
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs2327017; hg19: chr6-7650232;