2-76116064-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000287474 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670606.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287474	ENST00000670606.1		n.832+33372T>C		intron	N/A

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

African (AFR) AF: 0.220 AC: 9133 AN: 41518

American (AMR) AF: 0.225 AC: 3446 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3464

East Asian (EAS) AF: 0.495 AC: 2553 AN: 5156

South Asian (SAS) AF: 0.149 AC: 716 AN: 4820

European-Finnish (FIN) AF: 0.196 AC: 2073 AN: 10574

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8483 AN: 67996

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.143 Hom.: 7857

Bravo AF: 0.190

Asia WGS AF: 0.340 AC: 1180 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.75
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs10496200; hg19: chr2-76343190;