chr6-137652212-G-A

Position:

• chr6-137652212-G-A

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 0.0891 in 152,228 control chromosomes in the GnomAD database, including 646 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 0.089 (646 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.103 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: 0.0890 AC: 13543 AN: 152110 Hom.: 642 Cov.: 31

Gnomad AFR AF: 0.0936

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.0891 AC: 13558 AN: 152228 Hom.: 646 Cov.: 31 AF XY: 0.0893 AC XY: 6644 AN XY: 74432

Gnomad4 AFR AF: 0.0934

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.0835

Gnomad4 NFE AF: 0.0880

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0754 Hom.: 156

Bravo AF: 0.0927

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17066681; hg19: chr6-137973349;