rs2187688

chr6-32904224-A-Gchr6-32904224-A-T

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 0.525 in 151,944 control chromosomes in the GnomAD database, including 21,214 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 0.52 (21214 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 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: 0.525 AC: 79677 AN: 151826 Hom.: 21189 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.525 AC: 79752 AN: 151944 Hom.: 21214 Cov.: 31 AF XY: 0.524 AC XY: 38936 AN XY: 74264

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.506

Alfa AF: 0.522 Hom.: 3165

Bravo AF: 0.521

Asia WGS AF: 0.567 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2187688; hg19: chr6-32872001;