rs12532960

Positions:

• chr7-42286026-G-T

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 0.0937 in 152,150 control chromosomes in the GnomAD database, including 798 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 0.094 (798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.603

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.132 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: 0.0938 AC: 14265 AN: 152032 Hom.: 799 Cov.: 32

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0937 AC: 14261 AN: 152150 Hom.: 798 Cov.: 32 AF XY: 0.0931 AC XY: 6924 AN XY: 74374

Gnomad4 AFR AF: 0.0332

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.0288

Gnomad4 SAS AF: 0.0480

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.104

Alfa AF: 0.117 Hom.: 1055

Bravo AF: 0.0925

Asia WGS AF: 0.0490 AC: 168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12532960; hg19: chr7-42325625;