rs926774

Variant names:

• chr6-47153539-A-G
• rs926774

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 0.217 in 152,118 control chromosomes in the GnomAD database, including 4,314 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 0.22 (4314 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.217 AC: 33009 AN: 152000 Hom.: 4303 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.217 AC: 33045 AN: 152118 Hom.: 4314 Cov.: 33 AF XY: 0.225 AC XY: 16770 AN XY: 74376

African (AFR) AF: 0.267 AC: 11086 AN: 41448

American (AMR) AF: 0.324 AC: 4954 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3470

East Asian (EAS) AF: 0.471 AC: 2436 AN: 5174

South Asian (SAS) AF: 0.160 AC: 774 AN: 4828

European-Finnish (FIN) AF: 0.276 AC: 2916 AN: 10576

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9603 AN: 68022

Other (OTH) AF: 0.197 AC: 416 AN: 2114

Alfa AF: 0.167 Hom.: 11595

Bravo AF: 0.231

Asia WGS AF: 0.273 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.51
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs926774; hg19: chr6-47121275;