rs2127675

Variant names:

• chr6-32883073-A-G
• rs2127675

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 0.36 in 152,042 control chromosomes in the GnomAD database, including 10,031 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 0.36 (10031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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: 0.360 AC: 54655 AN: 151924 Hom.: 10023 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.360 AC: 54694 AN: 152042 Hom.: 10031 Cov.: 32 AF XY: 0.353 AC XY: 26271 AN XY: 74354

African (AFR) AF: 0.389 AC: 16110 AN: 41410

American (AMR) AF: 0.382 AC: 5836 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1394 AN: 5186

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4828

European-Finnish (FIN) AF: 0.304 AC: 3212 AN: 10570

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.358 AC: 24347 AN: 67976

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.365 Hom.: 7624

Bravo AF: 0.368

Asia WGS AF: 0.296 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.70
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs2127675; hg19: chr6-32850850;