chr2-105722179-G-C

Variant names:

• chr2-105722179-G-C
• rs955798
• ENST00000720028.1:n.90+13302C>G

Variant summary

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

The ENST00000720028.1(ENSG00000293937):​n.90+13302C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,974 control chromosomes in the GnomAD database, including 10,665 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 0.36 (10665 hom., cov: 32)
• Consequence: ENSG00000293937 ENST00000720028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 2 publications found

Genes affected

ENSG00000293937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720028.1. 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
	ENSG00000293937	ENST00000720028.1		n.90+13302C>G		intron	N/A
	ENSG00000293937	ENST00000720029.1		n.259+11981C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55395 AN: 151856 Hom.: 10649 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.365 AC: 55456 AN: 151974 Hom.: 10665 Cov.: 32 AF XY: 0.366 AC XY: 27213 AN XY: 74272

African (AFR) AF: 0.492 AC: 20381 AN: 41450

American (AMR) AF: 0.359 AC: 5489 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3468

East Asian (EAS) AF: 0.403 AC: 2075 AN: 5150

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4812

European-Finnish (FIN) AF: 0.359 AC: 3788 AN: 10560

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20224 AN: 67940

Other (OTH) AF: 0.342 AC: 721 AN: 2106

Alfa AF: 0.175 Hom.: 352

Bravo AF: 0.371

Asia WGS AF: 0.359 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.64
PhyloP100		-0.17

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: rs955798;

hg19: chr2-106338636;