rs17047733

Variant names:

• chr2-118083749-T-C
• rs17047733
• ENST00000747789.1:n.231+3764A>G

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+3764A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,174 control chromosomes in the GnomAD database, including 1,873 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 0.14 (1873 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616
• Publications: 5 publications found

Genes affected

ENSG00000297418 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747789.1. 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
	ENSG00000297418	ENST00000747789.1		n.231+3764A>G		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+4502A>G		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.271+3764A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21656 AN: 152054 Hom.: 1874 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.142 AC: 21660 AN: 152174 Hom.: 1873 Cov.: 32 AF XY: 0.141 AC XY: 10492 AN XY: 74406

African (AFR) AF: 0.201 AC: 8351 AN: 41514

American (AMR) AF: 0.195 AC: 2974 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1722 AN: 5172

South Asian (SAS) AF: 0.139 AC: 669 AN: 4820

European-Finnish (FIN) AF: 0.0833 AC: 883 AN: 10602

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0924 AC: 6285 AN: 67990

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.111 Hom.: 4693

Bravo AF: 0.157

Asia WGS AF: 0.198 AC: 687 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	6.4
DANN	Benign	0.82
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs17047733; hg19: chr2-118841325;