ENST00000758268.1:n.268-2432G>A

Variant names:

• chr1-207421598-G-A
• rs2135924
• ENST00000758268.1:n.268-2432G>A

Variant summary

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

The ENST00000758268.1(ENSG00000298838):​n.268-2432G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,094 control chromosomes in the GnomAD database, including 2,677 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 0.19 (2677 hom., cov: 32)
• Consequence: ENSG00000298838 ENST00000758268.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

Genes affected

ENSG00000298838 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372880	XR_922484.2	n.269-2432G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298838	ENST00000758268.1	n.268-2432G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28279 AN: 151976 Hom.: 2671 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.186 AC: 28306 AN: 152094 Hom.: 2677 Cov.: 32 AF XY: 0.183 AC XY: 13569 AN XY: 74348

African (AFR) AF: 0.186 AC: 7701 AN: 41488

American (AMR) AF: 0.155 AC: 2373 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3468

East Asian (EAS) AF: 0.105 AC: 545 AN: 5182

South Asian (SAS) AF: 0.165 AC: 797 AN: 4816

European-Finnish (FIN) AF: 0.167 AC: 1765 AN: 10560

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13720 AN: 67980

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.196 Hom.: 11046

Bravo AF: 0.186

Asia WGS AF: 0.138 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.7
DANN	Benign	0.90
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2135924; hg19: chr1-207594943; COSMIC: COSV60019705;