rs769178

Variant names:

• chr6-31579737-G-T
• rs769178

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0866 in 152,216 control chromosomes in the GnomAD database, including 821 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 0.087 (821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 50 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13154 AN: 152098 Hom.: 817 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0913

Gnomad OTH AF: 0.0966

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

GnomAD4 genome AF: 0.0866 AC: 13179 AN: 152216 Hom.: 821 Cov.: 32 AF XY: 0.0886 AC XY: 6595 AN XY: 74424

African (AFR) AF: 0.0299 AC: 1242 AN: 41552

American (AMR) AF: 0.171 AC: 2619 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3470

East Asian (EAS) AF: 0.134 AC: 692 AN: 5160

South Asian (SAS) AF: 0.133 AC: 640 AN: 4822

European-Finnish (FIN) AF: 0.0554 AC: 588 AN: 10616

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0913 AC: 6210 AN: 67994

Other (OTH) AF: 0.102 AC: 216 AN: 2114

Alfa AF: 0.0914 Hom.: 439

Bravo AF: 0.0918

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs769178; hg19: chr6-31547514;