rs2388956

Variant names:

• chr1-80018321-C-A
• rs2388956
• ENST00000644002.1:n.459+32225G>T

Variant summary

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

The ENST00000644002.1(ENSG00000285409):​n.459+32225G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.958 in 152,284 control chromosomes in the GnomAD database, including 70,133 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 0.96 (70133 hom., cov: 32)
• Consequence: ENSG00000285409 ENST00000644002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 2 publications found

Genes affected

ENSG00000285409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 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
ENSG00000285409	ENST00000644002.1	n.459+32225G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.958 AC: 145843 AN: 152166 Hom.: 70090 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.958 AC: 145939 AN: 152284 Hom.: 70133 Cov.: 32 AF XY: 0.955 AC XY: 71150 AN XY: 74468

African (AFR) AF: 0.929 AC: 38611 AN: 41560

American (AMR) AF: 0.967 AC: 14777 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3456 AN: 3470

East Asian (EAS) AF: 0.755 AC: 3907 AN: 5174

South Asian (SAS) AF: 0.900 AC: 4346 AN: 4830

European-Finnish (FIN) AF: 0.982 AC: 10424 AN: 10616

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67241 AN: 68028

Other (OTH) AF: 0.951 AC: 2011 AN: 2114

Alfa AF: 0.975 Hom.: 24065

Bravo AF: 0.955

Asia WGS AF: 0.832 AC: 2896 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.6
DANN	Benign	0.65
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs2388956; hg19: chr1-80484006;