rs2008312

Variant names:

• chr2-65227510-A-G
• rs2008312
• ENST00000650256.1:n.96T>C

Variant summary

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

The ENST00000650256.1(ENSG00000293332):​n.96T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,108 control chromosomes in the GnomAD database, including 9,149 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 0.33 (9149 hom., cov: 33)
• Consequence: ENSG00000293332 ENST00000650256.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 8 publications found

Genes affected

ENSG00000293332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650256.1. 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
	ENSG00000293332	ENST00000650256.1		n.96T>C		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000293332	ENST00000688491.2		n.96T>C		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000293332	ENST00000691402.2		n.137T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49850 AN: 151990 Hom.: 9125 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.328 AC: 49915 AN: 152108 Hom.: 9149 Cov.: 33 AF XY: 0.324 AC XY: 24064 AN XY: 74358

African (AFR) AF: 0.477 AC: 19797 AN: 41494

American (AMR) AF: 0.220 AC: 3355 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3472

East Asian (EAS) AF: 0.00521 AC: 27 AN: 5180

South Asian (SAS) AF: 0.190 AC: 914 AN: 4822

European-Finnish (FIN) AF: 0.304 AC: 3216 AN: 10568

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20573 AN: 67978

Other (OTH) AF: 0.299 AC: 632 AN: 2112

Alfa AF: 0.299 Hom.: 15321

Bravo AF: 0.325

Asia WGS AF: 0.158 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-1.7
PromoterAI		-0.0068	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2008312; hg19: chr2-65454644;