chr6-137131771-A-G

Variant names:

• chr6-137131771-A-G
• rs17066096

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 0.2 in 152,160 control chromosomes in the GnomAD database, including 3,214 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 0.20 (3214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 58 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 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: 0.201 AC: 30514 AN: 152042 Hom.: 3219 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.200 AC: 30506 AN: 152160 Hom.: 3214 Cov.: 32 AF XY: 0.198 AC XY: 14693 AN XY: 74392

African (AFR) AF: 0.146 AC: 6062 AN: 41538

American (AMR) AF: 0.203 AC: 3109 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3464

East Asian (EAS) AF: 0.0899 AC: 466 AN: 5184

South Asian (SAS) AF: 0.173 AC: 838 AN: 4832

European-Finnish (FIN) AF: 0.185 AC: 1951 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16557 AN: 67968

Other (OTH) AF: 0.193 AC: 408 AN: 2114

Alfa AF: 0.229 Hom.: 15723

Bravo AF: 0.198

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.83
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs17066096; hg19: chr6-137452908;