rs2008312

Positions:

• chr2-65227510-A-G

Variant summary

Our verdict is Benign. Variant got -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: ENST00000650256.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907779	XR_007086461.1	n.90T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650256.1	n.96T>C		non_coding_transcript_exon_variant	1/4
	ENST00000688491.1	n.90T>C		non_coding_transcript_exon_variant	1/4
	ENST00000691402.1	n.90T>C		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.00521

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.299

Alfa AF: 0.297 Hom.: 11043

Bravo AF: 0.325

Asia WGS AF: 0.158 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2008312; hg19: chr2-65454644;