rs12538002

chr7-6571702-A-G

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 0.395 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.403

Alfa AF: 0.355 Hom.: 7258

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12538002; hg19: chr7-6611333;