rs12538002

Variant names:

• chr7-6571702-A-G
• rs12538002

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 0.395 in 152,062 control chromosomes in the GnomAD database, including 12,999 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 0.40 (12999 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 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: 0.395 AC: 60036 AN: 151944 Hom.: 12964 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.395 AC: 60123 AN: 152062 Hom.: 12999 Cov.: 32 AF XY: 0.393 AC XY: 29218 AN XY: 74330

African (AFR) AF: 0.570 AC: 23656 AN: 41470

American (AMR) AF: 0.446 AC: 6816 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3472

East Asian (EAS) AF: 0.244 AC: 1257 AN: 5162

South Asian (SAS) AF: 0.326 AC: 1573 AN: 4824

European-Finnish (FIN) AF: 0.271 AC: 2863 AN: 10574

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21642 AN: 67976

Other (OTH) AF: 0.403 AC: 851 AN: 2112

Alfa AF: 0.358 Hom.: 10551

Bravo AF: 0.417

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs12538002; hg19: chr7-6611333;