rs10514102

Variant names:

• chr18-73947584-G-T
• rs10514102
• ENST00000581541.1:n.122-32555C>A

Variant summary

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

The ENST00000581541.1(ENSG00000263655):​n.122-32555C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0453 in 152,062 control chromosomes in the GnomAD database, including 174 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 0.045 (174 hom., cov: 32)
• Consequence: ENSG00000263655 ENST00000581541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 1 publications found

Genes affected

ENSG00000263655 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0656 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
ENSG00000263655	ENST00000581541.1	n.122-32555C>A		intron_variant	Intron 1 of 2	3
ENSG00000263655	ENST00000753906.1	n.179+3474C>A		intron_variant	Intron 2 of 3
ENSG00000263655	ENST00000753907.1	n.190+3474C>A		intron_variant	Intron 1 of 2
ENSG00000287314	ENST00000753825.1	n.-225G>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6873 AN: 151944 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.00829

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.00964

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0453 AC: 6889 AN: 152062 Hom.: 174 Cov.: 32 AF XY: 0.0440 AC XY: 3273 AN XY: 74322

African (AFR) AF: 0.0677 AC: 2809 AN: 41486

American (AMR) AF: 0.0279 AC: 426 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3466

East Asian (EAS) AF: 0.00830 AC: 43 AN: 5178

South Asian (SAS) AF: 0.0671 AC: 322 AN: 4796

European-Finnish (FIN) AF: 0.00964 AC: 102 AN: 10578

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0424 AC: 2884 AN: 67978

Other (OTH) AF: 0.0455 AC: 96 AN: 2108

Alfa AF: 0.0458 Hom.: 19

Bravo AF: 0.0466

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	10
DANN	Benign	0.67
PhyloP100		-0.043
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10514102; hg19: chr18-71614819;