rs2359382

Variant names:

• chr1-34529427-G-A
• rs2359382
• ENST00000824030.1:n.136+29687C>T

Variant summary

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

The ENST00000824030.1(ENSG00000307130):​n.136+29687C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,042 control chromosomes in the GnomAD database, including 46,304 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 0.77 (46304 hom., cov: 31)
• Consequence: ENSG00000307130 ENST00000824030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 3 publications found

Genes affected

ENSG00000307130 (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 = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378641	XR_001737964.2	n.577+18152C>T		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307130	ENST00000824030.1	n.136+29687C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117262 AN: 151924 Hom.: 46246 Cov.: 31

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.772 AC: 117381 AN: 152042 Hom.: 46304 Cov.: 31 AF XY: 0.775 AC XY: 57601 AN XY: 74312

African (AFR) AF: 0.918 AC: 38111 AN: 41512

American (AMR) AF: 0.804 AC: 12288 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2453 AN: 3466

East Asian (EAS) AF: 0.983 AC: 5048 AN: 5134

South Asian (SAS) AF: 0.809 AC: 3889 AN: 4806

European-Finnish (FIN) AF: 0.686 AC: 7237 AN: 10548

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46013 AN: 67972

Other (OTH) AF: 0.745 AC: 1574 AN: 2114

Alfa AF: 0.738 Hom.: 14209

Bravo AF: 0.786

Asia WGS AF: 0.903 AC: 3140 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	0.18
DANN	Benign	0.60
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2359382; hg19: chr1-34995028;