rs1779876

Variant names:

• chr10-36359112-T-G
• rs1779876

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 0.117 in 152,166 control chromosomes in the GnomAD database, including 1,207 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 0.12 (1207 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.199 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: 0.117 AC: 17750 AN: 152048 Hom.: 1203 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0574

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.117 AC: 17785 AN: 152166 Hom.: 1207 Cov.: 32 AF XY: 0.119 AC XY: 8850 AN XY: 74406

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.0574

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.0850

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0924 Hom.: 1702

Bravo AF: 0.132

Asia WGS AF: 0.122 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1779876; hg19: chr10-36648040;