rs12531052

Variant names:

• chr7-42389030-G-A
• rs12531052

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 0.0536 in 152,228 control chromosomes in the GnomAD database, including 277 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 0.054 (277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0946 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: 0.0537 AC: 8164 AN: 152110 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0754

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0536 AC: 8161 AN: 152228 Hom.: 277 Cov.: 32 AF XY: 0.0550 AC XY: 4097 AN XY: 74430

African (AFR) AF: 0.0185 AC: 770 AN: 41558

American (AMR) AF: 0.0987 AC: 1510 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3468

East Asian (EAS) AF: 0.0213 AC: 110 AN: 5166

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4828

European-Finnish (FIN) AF: 0.0754 AC: 799 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0667 AC: 4532 AN: 67990

Other (OTH) AF: 0.0621 AC: 131 AN: 2110

Alfa AF: 0.0623 Hom.: 62

Bravo AF: 0.0553

Asia WGS AF: 0.0320 AC: 111 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	1.8
DANN	Benign	0.83
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs12531052; hg19: chr7-42428629;