rs952312

Variant names:

• chr1-80018289-A-G
• rs952312
• ENST00000644002.1:n.459+32257T>C

Variant summary

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

The ENST00000644002.1(ENSG00000285409):​n.459+32257T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,146 control chromosomes in the GnomAD database, including 1,889 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 0.14 (1889 hom., cov: 32)
• Consequence: ENSG00000285409 ENST00000644002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 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+32257T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21288 AN: 152028 Hom.: 1884 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.140 AC: 21314 AN: 152146 Hom.: 1889 Cov.: 32 AF XY: 0.144 AC XY: 10680 AN XY: 74400

African (AFR) AF: 0.240 AC: 9939 AN: 41480

American (AMR) AF: 0.0966 AC: 1475 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1248 AN: 5180

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4820

European-Finnish (FIN) AF: 0.0817 AC: 865 AN: 10590

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0825 AC: 5609 AN: 68012

Other (OTH) AF: 0.139 AC: 293 AN: 2114

Alfa AF: 0.103 Hom.: 806

Bravo AF: 0.144

Asia WGS AF: 0.236 AC: 822 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.79
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs952312; hg19: chr1-80483974;