rs2494312

Variant names:

• chr1-194527460-C-T
• rs2494312
• ENST00000789595.1:n.437+9430C>T

Variant summary

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

The ENST00000789595.1(ENSG00000302795):​n.437+9430C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,218 control chromosomes in the GnomAD database, including 64,587 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 0.92 (64587 hom., cov: 31)
• Consequence: ENSG00000302795 ENST00000789595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 1 publications found

Genes affected

ENSG00000302795 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789595.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302795	ENST00000789595.1		n.437+9430C>T		intron	N/A
	ENSG00000302795	ENST00000789596.1		n.295+9430C>T		intron	N/A
	ENSG00000302795	ENST00000789597.1		n.59+5118C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140032 AN: 152100 Hom.: 64544 Cov.: 31

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.921 AC: 140127 AN: 152218 Hom.: 64587 Cov.: 31 AF XY: 0.921 AC XY: 68524 AN XY: 74402

African (AFR) AF: 0.954 AC: 39644 AN: 41562

American (AMR) AF: 0.948 AC: 14485 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3318 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5164 AN: 5166

South Asian (SAS) AF: 0.953 AC: 4604 AN: 4830

European-Finnish (FIN) AF: 0.868 AC: 9184 AN: 10578

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60591 AN: 68016

Other (OTH) AF: 0.931 AC: 1968 AN: 2114

Alfa AF: 0.904 Hom.: 34639

Bravo AF: 0.927

Asia WGS AF: 0.964 AC: 3351 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.39
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2494312; hg19: chr1-194496590;