rs10928927

Variant names:

• chr2-129710793-C-T
• rs10928927
• ENST00000765571.1:n.167C>T

Variant summary

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

The ENST00000765571.1(ENSG00000299679):​n.167C>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 0.705 in 152,034 control chromosomes in the GnomAD database, including 40,587 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 0.71 (40587 hom., cov: 32)
• Consequence: ENSG00000299679 ENST00000765571.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 7 publications found

Genes affected

ENSG00000299679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.837 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
ENSG00000299679	ENST00000765571.1	n.167C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000299698	ENST00000765702.1	n.395G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000299679	ENST00000765570.1	n.200-241C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107180 AN: 151916 Hom.: 40588 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.705 AC: 107205 AN: 152034 Hom.: 40587 Cov.: 32 AF XY: 0.707 AC XY: 52521 AN XY: 74298

African (AFR) AF: 0.406 AC: 16815 AN: 41464

American (AMR) AF: 0.748 AC: 11441 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2987 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3719 AN: 5116

South Asian (SAS) AF: 0.687 AC: 3307 AN: 4812

European-Finnish (FIN) AF: 0.860 AC: 9102 AN: 10586

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57257 AN: 67972

Other (OTH) AF: 0.740 AC: 1563 AN: 2112

Alfa AF: 0.805 Hom.: 136386

Bravo AF: 0.683

Asia WGS AF: 0.657 AC: 2285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.65
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs10928927; hg19: chr2-130468366;