chr6-137579612-A-G

Variant names:

• chr6-137579612-A-G
• rs7758499

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 0.228 in 152,130 control chromosomes in the GnomAD database, including 4,266 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 0.23 (4266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 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: 0.228 AC: 34704 AN: 152012 Hom.: 4269 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.228 AC: 34720 AN: 152130 Hom.: 4266 Cov.: 32 AF XY: 0.236 AC XY: 17575 AN XY: 74374

African (AFR) AF: 0.235 AC: 9755 AN: 41502

American (AMR) AF: 0.177 AC: 2706 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3466

East Asian (EAS) AF: 0.526 AC: 2716 AN: 5160

South Asian (SAS) AF: 0.243 AC: 1173 AN: 4820

European-Finnish (FIN) AF: 0.338 AC: 3576 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13545 AN: 67994

Other (OTH) AF: 0.228 AC: 482 AN: 2114

Alfa AF: 0.202 Hom.: 727

Bravo AF: 0.218

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.33
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs7758499; hg19: chr6-137900749;