chr2-176908534-C-G

Variant names:

• chr2-176908534-C-G
• rs4894215
• ENST00000795314.1:n.323+16147C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000795314.1(ENSG00000303534):​n.323+16147C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,034 control chromosomes in the GnomAD database, including 16,480 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 0.45 (16480 hom., cov: 32)
• Consequence: ENSG00000303534 ENST00000795314.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 4 publications found

Genes affected

ENSG00000303534 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795314.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303534	ENST00000795314.1		n.323+16147C>G		intron	N/A
	ENSG00000303534	ENST00000795315.1		n.100+16147C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68151 AN: 151916 Hom.: 16462 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.449 AC: 68220 AN: 152034 Hom.: 16480 Cov.: 32 AF XY: 0.457 AC XY: 33954 AN XY: 74298

African (AFR) AF: 0.362 AC: 15003 AN: 41478

American (AMR) AF: 0.551 AC: 8407 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3472

East Asian (EAS) AF: 0.955 AC: 4944 AN: 5178

South Asian (SAS) AF: 0.651 AC: 3136 AN: 4818

European-Finnish (FIN) AF: 0.476 AC: 5029 AN: 10556

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28952 AN: 67962

Other (OTH) AF: 0.424 AC: 894 AN: 2108

Alfa AF: 0.326 Hom.: 902

Bravo AF: 0.447

Asia WGS AF: 0.727 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	19
DANN	Benign	0.50
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs4894215; hg19: chr2-177773262;