chr2-76116064-T-C

Variant names:

• chr2-76116064-T-C
• rs10496200
• ENST00000670606.1:n.832+33372T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670606.1(ENSG00000287474):​n.832+33372T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,128 control chromosomes in the GnomAD database, including 2,952 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 0.18 (2952 hom., cov: 32)
• Consequence: ENSG00000287474 ENST00000670606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768

Genes affected

ENSG00000287474 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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
ENSG00000287474	ENST00000670606.1	n.832+33372T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27220 AN: 152010 Hom.: 2932 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.179 AC: 27288 AN: 152128 Hom.: 2952 Cov.: 32 AF XY: 0.184 AC XY: 13651 AN XY: 74362

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.168

Alfa AF: 0.136 Hom.: 3617

Bravo AF: 0.190

Asia WGS AF: 0.340 AC: 1180 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496200; hg19: chr2-76343190;