rs2579176

Variant names:

• chr10-77769592-A-G
• rs2579176

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 0.261 in 152,042 control chromosomes in the GnomAD database, including 5,967 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 0.26 (5967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 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: 0.262 AC: 39766 AN: 151924 Hom.: 5970 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.261 AC: 39751 AN: 152042 Hom.: 5967 Cov.: 32 AF XY: 0.259 AC XY: 19209 AN XY: 74298

African (AFR) AF: 0.117 AC: 4835 AN: 41488

American (AMR) AF: 0.255 AC: 3895 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3466

East Asian (EAS) AF: 0.191 AC: 990 AN: 5174

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4812

European-Finnish (FIN) AF: 0.258 AC: 2722 AN: 10546

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23594 AN: 67960

Other (OTH) AF: 0.292 AC: 617 AN: 2114

Alfa AF: 0.289 Hom.: 2291

Bravo AF: 0.255

Asia WGS AF: 0.242 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.78
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2579176; hg19: chr10-79529350; COSMIC: COSV70882936;