rs2327017

chr6-7649999-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;