rs7758499

Positions:

• chr6-137579612-A-G

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 0.228 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.228

Alfa AF: 0.201 Hom.: 634

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7758499; hg19: chr6-137900749;