rs2190712

Variant names:

• chr17-71493903-A-G
• rs2190712
• ENST00000722984.1:n.218+3760A>G

Variant summary

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

The ENST00000722984.1(ENSG00000294342):​n.218+3760A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,128 control chromosomes in the GnomAD database, including 2,925 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 0.19 (2925 hom., cov: 31)
• Consequence: ENSG00000294342 ENST00000722984.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 1 publications found

Genes affected

ENSG00000294342 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294342	ENST00000722984.1	n.218+3760A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28773 AN: 152010 Hom.: 2926 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.189 AC: 28782 AN: 152128 Hom.: 2925 Cov.: 31 AF XY: 0.186 AC XY: 13831 AN XY: 74360

African (AFR) AF: 0.122 AC: 5084 AN: 41552

American (AMR) AF: 0.174 AC: 2649 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3468

East Asian (EAS) AF: 0.0425 AC: 220 AN: 5176

South Asian (SAS) AF: 0.178 AC: 858 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2269 AN: 10580

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

European-Non Finnish (NFE) AF: 0.240 AC: 16287 AN: 67954

Other (OTH) AF: 0.217 AC: 457 AN: 2108

Alfa AF: 0.215 Hom.: 2894

Bravo AF: 0.180

Asia WGS AF: 0.106 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.26
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2190712; hg19: chr17-69490044;