6-137643560-A-G

Variant names:

• chr6-137643560-A-G
• rs62432712

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 0.153 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0897 AC: 3729 AN: 41558

American (AMR) AF: 0.121 AC: 1856 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3466

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5192

South Asian (SAS) AF: 0.121 AC: 584 AN: 4814

European-Finnish (FIN) AF: 0.178 AC: 1882 AN: 10594

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14198 AN: 68006

Other (OTH) AF: 0.155 AC: 328 AN: 2114

Alfa AF: 0.100 Hom.: 173

Bravo AF: 0.145

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.75
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs62432712; hg19: chr6-137964697;