2-172090013-G-C

Variant names:

• chr2-172090013-G-C
• rs813720
• ENST00000715284.1:n.308+3327C>G

Variant summary

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

The ENST00000715284.1(ENSG00000288958):​n.308+3327C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,110 control chromosomes in the GnomAD database, including 15,401 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 0.42 (15401 hom., cov: 33)
• Consequence: ENSG00000288958 ENST00000715284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715284.1. 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	ENST00000715284.1		n.308+3327C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64091 AN: 151992 Hom.: 15374 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.422 AC: 64164 AN: 152110 Hom.: 15401 Cov.: 33 AF XY: 0.416 AC XY: 30956 AN XY: 74348

African (AFR) AF: 0.664 AC: 27568 AN: 41500

American (AMR) AF: 0.334 AC: 5102 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1333 AN: 3466

East Asian (EAS) AF: 0.272 AC: 1406 AN: 5178

South Asian (SAS) AF: 0.304 AC: 1461 AN: 4812

European-Finnish (FIN) AF: 0.356 AC: 3766 AN: 10572

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22262 AN: 67970

Other (OTH) AF: 0.415 AC: 877 AN: 2114

Alfa AF: 0.211 Hom.: 433

Bravo AF: 0.433

Asia WGS AF: 0.352 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.068
DANN	Benign	0.77
PhyloP100		-1.7

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: rs813720;

hg19: chr2-172954741;