17-55617411-C-T

Variant names:

• chr17-55617411-C-T
• rs10515103
• ENST00000685048.2:n.338-114C>T

Variant summary

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

The ENST00000685048.2(ENSG00000289016):​n.338-114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,232 control chromosomes in the GnomAD database, including 230 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 0.049 (230 hom., cov: 32)
• Consequence: ENSG00000289016 ENST00000685048.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 1 publications found

Genes affected

ENSG00000289016 (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 (AFR) allele frequency at 95% confidence interval = 0.0662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927389	XR_001752944.2	n.110-114C>T		intron_variant	Intron 1 of 4
LOC101927389	XR_243722.5	n.110-114C>T		intron_variant	Intron 1 of 4
LOC101927389	XR_934869.3	n.110-114C>T		intron_variant	Intron 1 of 5
LOC101927389	XR_934870.3	n.110-114C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289016	ENST00000685048.2	n.338-114C>T		intron_variant	Intron 1 of 4
ENSG00000289016	ENST00000690551.1	n.90-114C>T		intron_variant	Intron 1 of 2
ENSG00000289016	ENST00000847279.1	n.116-114C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0491 AC: 7462 AN: 152114 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0456

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0491 AC: 7473 AN: 152232 Hom.: 230 Cov.: 32 AF XY: 0.0467 AC XY: 3476 AN XY: 74432

African (AFR) AF: 0.0683 AC: 2835 AN: 41532

American (AMR) AF: 0.0456 AC: 697 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0763 AC: 265 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4826

European-Finnish (FIN) AF: 0.0217 AC: 230 AN: 10602

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0470 AC: 3195 AN: 68004

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0143 Hom.: 4

Bravo AF: 0.0531

Asia WGS AF: 0.0150 AC: 52 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	0.026
DANN	Benign	0.26
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10515103; hg19: chr17-53694772;