2-169363371-A-G

Variant names:

• chr2-169363371-A-G
• rs3755166
• ENST00000831911.1:n.*106T>C

Variant summary

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

The ENST00000831911.1(ENSG00000308140):​n.*106T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,052 control chromosomes in the GnomAD database, including 30,287 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 0.63 (30287 hom., cov: 32)
• Consequence: ENSG00000308140 ENST00000831911.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 21 publications found

Genes affected

ENSG00000308140 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831911.1. 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
	ENSG00000308140	ENST00000831911.1		n.*106T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95430 AN: 151934 Hom.: 30231 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.628 AC: 95549 AN: 152052 Hom.: 30287 Cov.: 32 AF XY: 0.628 AC XY: 46686 AN XY: 74330

African (AFR) AF: 0.687 AC: 28508 AN: 41472

American (AMR) AF: 0.661 AC: 10098 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1949 AN: 3472

East Asian (EAS) AF: 0.570 AC: 2950 AN: 5174

South Asian (SAS) AF: 0.679 AC: 3269 AN: 4814

European-Finnish (FIN) AF: 0.556 AC: 5872 AN: 10570

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40949 AN: 67970

Other (OTH) AF: 0.636 AC: 1336 AN: 2102

Alfa AF: 0.613 Hom.: 79957

Bravo AF: 0.634

Asia WGS AF: 0.614 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.51
PhyloP100		-0.49

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: rs3755166;

hg19: chr2-170219881;