10-77769457-G-A

Variant names:

• chr10-77769457-G-A
• rs2579178

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 152,016 control chromosomes in the GnomAD database, including 5,951 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 (5951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 5 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39632 AN: 151898 Hom.: 5954 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.432

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: 0.294

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

GnomAD4 genome AF: 0.261 AC: 39617 AN: 152016 Hom.: 5951 Cov.: 32 AF XY: 0.258 AC XY: 19158 AN XY: 74294

African (AFR) AF: 0.114 AC: 4738 AN: 41476

American (AMR) AF: 0.254 AC: 3881 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1253 AN: 3462

East Asian (EAS) AF: 0.191 AC: 987 AN: 5158

South Asian (SAS) AF: 0.283 AC: 1361 AN: 4804

European-Finnish (FIN) AF: 0.258 AC: 2725 AN: 10542

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

European-Non Finnish (NFE) AF: 0.347 AC: 23577 AN: 67984

Other (OTH) AF: 0.291 AC: 616 AN: 2114

Alfa AF: 0.290 Hom.: 955

Bravo AF: 0.254

Asia WGS AF: 0.241 AC: 841 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	2.6
DANN	Benign	0.74
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs2579178; hg19: chr10-79529215;