rs2327017

Variant names:

• chr6-7649999-C-A
• rs2327017

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.597 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

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.675

Alfa AF: 0.644 Hom.: 15201

Bravo AF: 0.593

Asia WGS AF: 0.672 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2327017; hg19: chr6-7650232;