rs7747594

Variant names:

• chr6-45779785-G-A
• rs7747594

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 0.0584 in 152,206 control chromosomes in the GnomAD database, including 468 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 0.058 (468 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0582 AC: 8852 AN: 152088 Hom.: 463 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.00616

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.0207

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0584 AC: 8891 AN: 152206 Hom.: 468 Cov.: 31 AF XY: 0.0583 AC XY: 4337 AN XY: 74436

African (AFR) AF: 0.129 AC: 5336 AN: 41500

American (AMR) AF: 0.0815 AC: 1247 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5184

South Asian (SAS) AF: 0.0515 AC: 248 AN: 4814

European-Finnish (FIN) AF: 0.0207 AC: 220 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0241 AC: 1640 AN: 68002

Other (OTH) AF: 0.0468 AC: 99 AN: 2116

Alfa AF: 0.0372 Hom.: 95

Bravo AF: 0.0656

Asia WGS AF: 0.0380 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.53
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs7747594; hg19: chr6-45747522;