chr2-212719964-C-A

Variant names:

• chr2-212719964-C-A
• rs10932444
• ENST00000765929.1:n.500G>T

Variant summary

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

The ENST00000765929.1(ENSG00000299731):​n.500G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,088 control chromosomes in the GnomAD database, including 40,798 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 0.73 (40798 hom., cov: 32)
• Consequence: ENSG00000299731 ENST00000765929.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 5 publications found

Genes affected

ENSG00000299731 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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
ENSG00000299731	ENST00000765929.1	n.500G>T		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000273118	ENST00000415387.1	n.382-138556G>T		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110590 AN: 151970 Hom.: 40772 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.728 AC: 110657 AN: 152088 Hom.: 40798 Cov.: 32 AF XY: 0.728 AC XY: 54114 AN XY: 74354

African (AFR) AF: 0.601 AC: 24899 AN: 41460

American (AMR) AF: 0.763 AC: 11663 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2553 AN: 3466

East Asian (EAS) AF: 0.823 AC: 4262 AN: 5178

South Asian (SAS) AF: 0.723 AC: 3487 AN: 4822

European-Finnish (FIN) AF: 0.808 AC: 8556 AN: 10590

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52658 AN: 67976

Other (OTH) AF: 0.733 AC: 1545 AN: 2108

Alfa AF: 0.755 Hom.: 75322

Bravo AF: 0.718

Asia WGS AF: 0.791 AC: 2748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.29
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs10932444; hg19: chr2-213584688;