ENST00000750357.1:n.271-18808T>C

Variant names:

• chr2-200238728-A-G
• rs296796
• ENST00000750357.1:n.271-18808T>C

Variant summary

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

The ENST00000750357.1(ENSG00000297701):​n.271-18808T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,054 control chromosomes in the GnomAD database, including 26,237 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 0.58 (26237 hom., cov: 32)
• Consequence: ENSG00000297701 ENST00000750357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 3 publications found

Genes affected

ENSG00000297701 (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 (SAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750357.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297701	ENST00000750357.1		n.271-18808T>C		intron	N/A
	ENSG00000297701	ENST00000750358.1		n.113-18808T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88566 AN: 151936 Hom.: 26228 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.583 AC: 88601 AN: 152054 Hom.: 26237 Cov.: 32 AF XY: 0.578 AC XY: 42939 AN XY: 74312

African (AFR) AF: 0.624 AC: 25863 AN: 41450

American (AMR) AF: 0.426 AC: 6500 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2257 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2617 AN: 5164

South Asian (SAS) AF: 0.698 AC: 3369 AN: 4824

European-Finnish (FIN) AF: 0.493 AC: 5210 AN: 10566

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.601 AC: 40835 AN: 67994

Other (OTH) AF: 0.580 AC: 1226 AN: 2114

Alfa AF: 0.599 Hom.: 6135

Bravo AF: 0.572

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.76
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs296796; hg19: chr2-201103451;