rs2187818

Positions:

• chr6-32427791-G-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 0.365 in 151,924 control chromosomes in the GnomAD database, including 10,584 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 0.37 (10584 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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 (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55505 AN: 151806 Hom.: 10578 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.365 AC: 55527 AN: 151924 Hom.: 10584 Cov.: 31 AF XY: 0.367 AC XY: 27273 AN XY: 74248

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.390

Alfa AF: 0.399 Hom.: 16786

Bravo AF: 0.371

Asia WGS AF: 0.444 AC: 1545 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	0.90
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2187818; hg19: chr6-32395568;