rs2116050

Variant names:

• chr2-67845631-G-A
• rs2116050
• ENST00000751172.1:n.*91C>T

Variant summary

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

The ENST00000751172.1(ENSG00000297812):​n.*91C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,020 control chromosomes in the GnomAD database, including 27,384 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 0.59 (27384 hom., cov: 32)
• Consequence: ENSG00000297812 ENST00000751172.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 5 publications found

Genes affected

ENSG00000297812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751172.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297812	ENST00000751172.1		n.*91C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89962 AN: 151902 Hom.: 27344 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.592 AC: 90056 AN: 152020 Hom.: 27384 Cov.: 32 AF XY: 0.588 AC XY: 43665 AN XY: 74308

African (AFR) AF: 0.743 AC: 30825 AN: 41462

American (AMR) AF: 0.510 AC: 7785 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1813 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3022 AN: 5168

South Asian (SAS) AF: 0.483 AC: 2330 AN: 4820

European-Finnish (FIN) AF: 0.550 AC: 5797 AN: 10540

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36479 AN: 67974

Other (OTH) AF: 0.570 AC: 1203 AN: 2112

Alfa AF: 0.546 Hom.: 14046

Bravo AF: 0.602

Asia WGS AF: 0.577 AC: 2007 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.78
DANN	Benign	0.61
PhyloP100		0.037

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2116050;

hg19: chr2-68072763;