rs2579177

chr10-77769487-C-T

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 152,166 control chromosomes in the GnomAD database, including 5,965 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 (5965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39742 AN: 152048 Hom.: 5968 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.192

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: 39727 AN: 152166 Hom.: 5965 Cov.: 32 AF XY: 0.258 AC XY: 19210 AN XY: 74394

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.255

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: 0.292

Alfa AF: 0.305 Hom.: 1005

Bravo AF: 0.254

Asia WGS AF: 0.242 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.089
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2579177; hg19: chr10-79529245;