chr2-150987464-T-C

Variant names:

• chr2-150987464-T-C
• rs989414
• ENST00000425983.1:n.10+4949T>C

Variant summary

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

The ENST00000425983.1(ENSG00000228064):​n.10+4949T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,172 control chromosomes in the GnomAD database, including 58,510 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 0.87 (58510 hom., cov: 32)
• Consequence: ENSG00000228064 ENST00000425983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• Publications: 2 publications found

Genes affected

ENSG00000228064 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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
ENSG00000228064	ENST00000425983.1	n.10+4949T>C		intron_variant	Intron 1 of 3	5
ENSG00000222031	ENST00000812493.1	n.182-10169A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132661 AN: 152054 Hom.: 58468 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.872 AC: 132757 AN: 152172 Hom.: 58510 Cov.: 32 AF XY: 0.875 AC XY: 65047 AN XY: 74368

African (AFR) AF: 0.743 AC: 30831 AN: 41478

American (AMR) AF: 0.914 AC: 13972 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3072 AN: 3470

East Asian (EAS) AF: 0.945 AC: 4885 AN: 5168

South Asian (SAS) AF: 0.841 AC: 4052 AN: 4820

European-Finnish (FIN) AF: 0.961 AC: 10190 AN: 10600

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62753 AN: 68030

Other (OTH) AF: 0.877 AC: 1849 AN: 2108

Alfa AF: 0.898 Hom.: 16011

Bravo AF: 0.865

Asia WGS AF: 0.884 AC: 3074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.48
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs989414; hg19: chr2-151843978;