ENST00000438963.2:n.782-4904T>C

Variant names:

• chr2-175457761-T-C
• rs2437896
• ENST00000438963.2:n.782-4904T>C

Variant summary

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

The ENST00000438963.2(ENSG00000229066):​n.782-4904T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,110 control chromosomes in the GnomAD database, including 14,235 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 0.41 (14235 hom., cov: 32)
• Consequence: ENSG00000229066 ENST00000438963.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 5 publications found

Genes affected

ENSG00000229066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373752	XR_923596.2	n.79+3077T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229066	ENST00000438963.2	n.782-4904T>C		intron_variant	Intron 2 of 2	3
ENSG00000229066	ENST00000653625.1	n.947+3077T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61948 AN: 151992 Hom.: 14208 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.408 AC: 62019 AN: 152110 Hom.: 14235 Cov.: 32 AF XY: 0.409 AC XY: 30374 AN XY: 74344

African (AFR) AF: 0.604 AC: 25045 AN: 41466

American (AMR) AF: 0.442 AC: 6758 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3468

East Asian (EAS) AF: 0.660 AC: 3408 AN: 5160

South Asian (SAS) AF: 0.433 AC: 2085 AN: 4816

European-Finnish (FIN) AF: 0.220 AC: 2332 AN: 10604

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19693 AN: 67990

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.337 Hom.: 27648

Bravo AF: 0.433

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2437896; hg19: chr2-176322489;