rs62432712

chr6-137643560-A-Gchr6-137643560-A-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 0.153 in 152,244 control chromosomes in the GnomAD database, including 2,038 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 0.15 (2038 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.759

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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: 0.153 AC: 23289 AN: 152126 Hom.: 2037 Cov.: 33

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.153 AC: 23289 AN: 152244 Hom.: 2038 Cov.: 33 AF XY: 0.149 AC XY: 11056 AN XY: 74446

Gnomad4 AFR AF: 0.0897

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.155

Alfa AF: 0.102 Hom.: 170

Bravo AF: 0.145

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.3
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62432712; hg19: chr6-137964697;