6-137810986-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0201 in 152,218 control chromosomes in the GnomAD database, including 42 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 0.020 (42 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0201 (3058/152218) while in subpopulation SAS AF= 0.049 (236/4816). AF 95% confidence interval is 0.0439. There are 42 homozygotes in gnomad4. There are 1455 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 42 gene

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: 0.0201 AC: 3054 AN: 152100 Hom.: 42 Cov.: 32

Gnomad AFR AF: 0.00519

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0187

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0201 AC: 3058 AN: 152218 Hom.: 42 Cov.: 32 AF XY: 0.0196 AC XY: 1455 AN XY: 74422

Gnomad4 AFR AF: 0.00518

Gnomad4 AMR AF: 0.0188

Gnomad4 ASJ AF: 0.0401

Gnomad4 EAS AF: 0.0129

Gnomad4 SAS AF: 0.0490

Gnomad4 FIN AF: 0.0160

Gnomad4 NFE AF: 0.0280

Gnomad4 OTH AF: 0.0170

Alfa AF: 0.0244 Hom.: 11

Bravo AF: 0.0183

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.9
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58905141; hg19: chr6-138132123;