rs17083037

Variant names:

• chr18-70713005-T-G
• rs17083037
• ENST00000745041.1:n.219-19333T>G

Variant summary

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

The ENST00000745041.1(ENSG00000297062):​n.219-19333T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0573 in 152,264 control chromosomes in the GnomAD database, including 280 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 0.057 (280 hom., cov: 32)
• Consequence: ENSG00000297062 ENST00000745041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 3 publications found

Genes affected

ENSG00000297062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0815 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
ENSG00000297062	ENST00000745041.1	n.219-19333T>G		intron_variant	Intron 2 of 2
ENSG00000297062	ENST00000745042.1	n.84-19131T>G		intron_variant	Intron 1 of 2
ENSG00000297062	ENST00000745044.1	n.71-19131T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0572 AC: 8705 AN: 152146 Hom.: 276 Cov.: 32

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0499

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0573 AC: 8732 AN: 152264 Hom.: 280 Cov.: 32 AF XY: 0.0562 AC XY: 4186 AN XY: 74448

African (AFR) AF: 0.0838 AC: 3481 AN: 41548

American (AMR) AF: 0.0437 AC: 669 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3472

East Asian (EAS) AF: 0.00561 AC: 29 AN: 5172

South Asian (SAS) AF: 0.0608 AC: 293 AN: 4820

European-Finnish (FIN) AF: 0.0473 AC: 502 AN: 10606

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0499 AC: 3394 AN: 68030

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

Alfa AF: 0.0522 Hom.: 261

Bravo AF: 0.0579

Asia WGS AF: 0.0450 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.56
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs17083037; hg19: chr18-68380241;