2-172092915-G-T

Variant names:

• chr2-172092915-G-T
• rs13390848
• ENST00000686675.1:n.741C>A

Variant summary

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

The ENST00000686675.1(ENSG00000288958):​n.741C>A 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 0.158 in 151,832 control chromosomes in the GnomAD database, including 2,332 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 0.16 (2332 hom., cov: 31)
• Consequence: ENSG00000288958 ENST00000686675.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 9 publications found

Genes affected

ENSG00000288958 (HGNC:58943):

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 (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000686675.1. 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
	ENSG00000288958	ENST00000686675.1		n.741C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288958	ENST00000715284.1		n.308+425C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23953 AN: 151714 Hom.: 2334 Cov.: 31

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.158 AC: 23949 AN: 151832 Hom.: 2332 Cov.: 31 AF XY: 0.154 AC XY: 11435 AN XY: 74170

African (AFR) AF: 0.0744 AC: 3077 AN: 41342

American (AMR) AF: 0.233 AC: 3552 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3464

East Asian (EAS) AF: 0.0891 AC: 461 AN: 5176

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4814

European-Finnish (FIN) AF: 0.0628 AC: 661 AN: 10530

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13363 AN: 67952

Other (OTH) AF: 0.188 AC: 396 AN: 2108

Alfa AF: 0.189 Hom.: 9821

Bravo AF: 0.166

Asia WGS AF: 0.170 AC: 591 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	0.48
DANN	Benign	0.77
PhyloP100		-2.0

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: rs13390848;

hg19: chr2-172957643;