rs1779876

Variant names:

• chr10-36359112-T-G
• rs1779876
• ENST00000426283.6:n.59+1189T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426283.6(ENSG00000237002):​n.59+1189T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000237002 ENST00000426283.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 11 publications found

Genes affected

ENSG00000237002 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000237002	ENST00000426283.6	n.59+1189T>G		intron_variant	Intron 1 of 3	3

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

African (AFR) AF: 0.149 AC: 6160 AN: 41480

American (AMR) AF: 0.205 AC: 3129 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0574 AC: 199 AN: 3466

East Asian (EAS) AF: 0.151 AC: 781 AN: 5156

South Asian (SAS) AF: 0.126 AC: 606 AN: 4820

European-Finnish (FIN) AF: 0.0771 AC: 818 AN: 10612

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0850 AC: 5779 AN: 68018

Other (OTH) AF: 0.120 AC: 254 AN: 2110

Alfa AF: 0.0972 Hom.: 3913

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
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs1779876; hg19: chr10-36648040;