chr18-10090774-T-C

Variant names:

• chr18-10090774-T-C
• rs17436811
• ENST00000685786.1:n.388+4549T>C

Variant summary

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

The ENST00000685786.1(ENSG00000265554):​n.388+4549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0386 in 152,314 control chromosomes in the GnomAD database, including 137 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 0.039 (137 hom., cov: 33)
• Consequence: ENSG00000265554 ENST00000685786.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 3 publications found

Genes affected

ENSG00000265554 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371984	XR_935136.3	n.666-2109T>C		intron_variant	Intron 1 of 2
LOC105371984	XR_935137.3	n.666-2139T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265554	ENST00000685786.1	n.388+4549T>C		intron_variant	Intron 1 of 1
ENSG00000265554	ENST00000751533.1	n.93+12469T>C		intron_variant	Intron 1 of 1
ENSG00000265554	ENST00000751534.1	n.82+12469T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5873 AN: 152196 Hom.: 136 Cov.: 33

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0310

Gnomad ASJ AF: 0.0544

Gnomad EAS AF: 0.00576

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0531

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0326

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

GnomAD4 genome AF: 0.0386 AC: 5878 AN: 152314 Hom.: 137 Cov.: 33 AF XY: 0.0380 AC XY: 2831 AN XY: 74474

African (AFR) AF: 0.0147 AC: 610 AN: 41570

American (AMR) AF: 0.0309 AC: 473 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0544 AC: 189 AN: 3472

East Asian (EAS) AF: 0.00578 AC: 30 AN: 5194

South Asian (SAS) AF: 0.0750 AC: 362 AN: 4826

European-Finnish (FIN) AF: 0.0531 AC: 564 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3574 AN: 68022

Other (OTH) AF: 0.0322 AC: 68 AN: 2110

Alfa AF: 0.0438 Hom.: 199

Bravo AF: 0.0331

Asia WGS AF: 0.0370 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs17436811; hg19: chr18-10090771;