17-67699983-C-G

Variant names:

• chr17-67699983-C-G
• rs2365403
• ENST00000832617.1:n.198-10610G>C

Variant summary

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

The ENST00000832617.1(ENSG00000288109):​n.198-10610G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,970 control chromosomes in the GnomAD database, including 2,868 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 (2868 hom., cov: 31)
• Consequence: ENSG00000288109 ENST00000832617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 4 publications found

Genes affected

ENSG00000288109 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928045	NR_188292.1	n.186-10610G>C		intron_variant	Intron 1 of 2
LOC101928045	NR_188293.1	n.38-10610G>C		intron_variant	Intron 1 of 2
LOC101928045	NR_188294.1	n.38-182G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288109	ENST00000832617.1	n.198-10610G>C		intron_variant	Intron 1 of 2
ENSG00000288109	ENST00000832618.1	n.212-10610G>C		intron_variant	Intron 1 of 2
ENSG00000288109	ENST00000832619.1	n.119-10610G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28897 AN: 151852 Hom.: 2865 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.190 AC: 28934 AN: 151970 Hom.: 2868 Cov.: 31 AF XY: 0.189 AC XY: 14060 AN XY: 74274

African (AFR) AF: 0.234 AC: 9683 AN: 41436

American (AMR) AF: 0.154 AC: 2357 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0812 AC: 282 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1384 AN: 5168

South Asian (SAS) AF: 0.0895 AC: 431 AN: 4814

European-Finnish (FIN) AF: 0.229 AC: 2419 AN: 10554

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11726 AN: 67970

Other (OTH) AF: 0.158 AC: 333 AN: 2102

Alfa AF: 0.177 Hom.: 329

Bravo AF: 0.189

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.45
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2365403; hg19: chr17-65696099;