rs28362434

Variant names:

• chr2-10438518-T-C
• rs28362434
• ENST00000757451.1:n.252-5164T>C

Variant summary

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

The ENST00000757451.1(ENSG00000298698):​n.252-5164T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,068 control chromosomes in the GnomAD database, including 3,276 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 0.20 (3276 hom., cov: 32)
• Consequence: ENSG00000298698 ENST00000757451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 1 publications found

Genes affected

ENSG00000298698 (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 (AFR) allele frequency at 95% confidence interval = 0.268 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
ENSG00000298698	ENST00000757451.1	n.252-5164T>C		intron_variant	Intron 1 of 1
ENSG00000298698	ENST00000757452.1	n.133-2924T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30181 AN: 151950 Hom.: 3272 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0228

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.199 AC: 30214 AN: 152068 Hom.: 3276 Cov.: 32 AF XY: 0.201 AC XY: 14921 AN XY: 74320

African (AFR) AF: 0.272 AC: 11283 AN: 41472

American (AMR) AF: 0.125 AC: 1903 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3470

East Asian (EAS) AF: 0.0226 AC: 117 AN: 5174

South Asian (SAS) AF: 0.163 AC: 787 AN: 4820

European-Finnish (FIN) AF: 0.261 AC: 2755 AN: 10562

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12376 AN: 67970

Other (OTH) AF: 0.172 AC: 362 AN: 2110

Alfa AF: 0.193 Hom.: 933

Bravo AF: 0.192

Asia WGS AF: 0.107 AC: 373 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	3.6
DANN	Benign	0.78
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs28362434; hg19: chr2-10578644;