rs2579178

Variant names:

• chr10-77769457-G-A
• rs2579178

Your query was ambiguous. Multiple possible variants found:

• chr10-77769457-G-A
• chr10-77769457-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.261 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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.291

Alfa AF: 0.296 Hom.: 948

Bravo AF: 0.254

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2579178; hg19: chr10-79529215;