rs12537998

Variant names:

• chr7-128271355-G-A
• rs12537998

Your query was ambiguous. Multiple possible variants found:

• chr7-128271355-G-A
• chr7-128271355-G-T

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 0.307 in 152,010 control chromosomes in the GnomAD database, including 8,930 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 0.31 (8930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 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: 0.308 AC: 46708 AN: 151892 Hom.: 8923 Cov.: 32

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.307 AC: 46727 AN: 152010 Hom.: 8930 Cov.: 32 AF XY: 0.314 AC XY: 23364 AN XY: 74290

African (AFR) AF: 0.0875 AC: 3629 AN: 41486

American (AMR) AF: 0.446 AC: 6825 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3472

East Asian (EAS) AF: 0.668 AC: 3451 AN: 5164

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4818

European-Finnish (FIN) AF: 0.399 AC: 4202 AN: 10542

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.365 AC: 24822 AN: 67924

Other (OTH) AF: 0.318 AC: 671 AN: 2112

Alfa AF: 0.344 Hom.: 13994

Bravo AF: 0.304

Asia WGS AF: 0.493 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.017
DANN	Benign	0.62
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs12537998; hg19: chr7-127911408;