chr2-233774704-A-G

Variant names:

• chr2-233774704-A-G
• rs11563250
• ENST00000755739.1:n.213-215T>C

Variant summary

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

The ENST00000755739.1(ENSG00000298478):​n.213-215T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,130 control chromosomes in the GnomAD database, including 1,313 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 0.12 (1313 hom., cov: 31)
• Consequence: ENSG00000298478 ENST00000755739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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.213-215T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17555 AN: 152012 Hom.: 1308 Cov.: 31

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.115 AC: 17565 AN: 152130 Hom.: 1313 Cov.: 31 AF XY: 0.117 AC XY: 8718 AN XY: 74360

African (AFR) AF: 0.0326 AC: 1353 AN: 41512

American (AMR) AF: 0.163 AC: 2495 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1070 AN: 5152

South Asian (SAS) AF: 0.198 AC: 951 AN: 4808

European-Finnish (FIN) AF: 0.151 AC: 1604 AN: 10588

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9194 AN: 68002

Other (OTH) AF: 0.132 AC: 279 AN: 2110

Alfa AF: 0.131 Hom.: 3514

Bravo AF: 0.111

Asia WGS AF: 0.198 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.73
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11563250; hg19: chr2-234683350;