2-233775246-C-T

Variant names:

• chr2-233775246-C-T
• rs4663972
• ENST00000755739.1:n.212+85G>A

Variant summary

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

The ENST00000755739.1(ENSG00000298478):​n.212+85G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,098 control chromosomes in the GnomAD database, including 43,400 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 0.75 (43400 hom., cov: 32)
• Consequence: ENSG00000298478 ENST00000755739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 10 publications found

Genes affected

ENSG00000298478 (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 = 0.855 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
ENSG00000298478	ENST00000755739.1	n.212+85G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114308 AN: 151980 Hom.: 43381 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.752 AC: 114374 AN: 152098 Hom.: 43400 Cov.: 32 AF XY: 0.759 AC XY: 56406 AN XY: 74354

African (AFR) AF: 0.662 AC: 27436 AN: 41456

American (AMR) AF: 0.750 AC: 11471 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2353 AN: 3466

East Asian (EAS) AF: 0.876 AC: 4513 AN: 5150

South Asian (SAS) AF: 0.820 AC: 3946 AN: 4814

European-Finnish (FIN) AF: 0.900 AC: 9546 AN: 10610

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52645 AN: 67994

Other (OTH) AF: 0.733 AC: 1549 AN: 2114

Alfa AF: 0.757 Hom.: 53245

Bravo AF: 0.735

Asia WGS AF: 0.821 AC: 2854 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	0.96
DANN	Benign	0.66
PhyloP100		-0.50
PromoterAI		0.0044	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4663972; hg19: chr2-234683892;