6-137646077-G-A

Variant names:

• chr6-137646077-G-A
• rs13192841

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 0.237 in 151,916 control chromosomes in the GnomAD database, including 4,525 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 0.24 (4525 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 63 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 (AMR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36009 AN: 151798 Hom.: 4521 Cov.: 30

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.237 AC: 36010 AN: 151916 Hom.: 4525 Cov.: 30 AF XY: 0.236 AC XY: 17500 AN XY: 74234

African (AFR) AF: 0.170 AC: 7025 AN: 41436

American (AMR) AF: 0.288 AC: 4391 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1185 AN: 3472

East Asian (EAS) AF: 0.0966 AC: 499 AN: 5168

South Asian (SAS) AF: 0.256 AC: 1229 AN: 4796

European-Finnish (FIN) AF: 0.223 AC: 2361 AN: 10564

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18368 AN: 67922

Other (OTH) AF: 0.241 AC: 507 AN: 2108

Alfa AF: 0.261 Hom.: 17418

Bravo AF: 0.242

Asia WGS AF: 0.155 AC: 541 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	5.3
DANN	Benign	0.82
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs13192841; hg19: chr6-137967214;