18-1125056-C-T

Variant names:

• chr18-1125056-C-T
• rs6505623
• ENST00000577719.5:n.308-8787C>T

Variant summary

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

The ENST00000577719.5(ENSG00000263551):​n.308-8787C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,936 control chromosomes in the GnomAD database, including 28,983 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 0.61 (28983 hom., cov: 32)
• Consequence: ENSG00000263551 ENST00000577719.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 3 publications found

Genes affected

ENSG00000263551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371953	XR_001753318.2	n.344-8787C>T		intron_variant	Intron 1 of 6
LOC105371953	XR_007066436.1	n.344-8787C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263551	ENST00000577719.5	n.308-8787C>T		intron_variant	Intron 1 of 3	3
ENSG00000263551	ENST00000579835.5	n.273-8787C>T		intron_variant	Intron 2 of 4	5
ENSG00000263551	ENST00000580781.5	n.307-8787C>T		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92963 AN: 151818 Hom.: 28967 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.612 AC: 93029 AN: 151936 Hom.: 28983 Cov.: 32 AF XY: 0.610 AC XY: 45269 AN XY: 74246

African (AFR) AF: 0.549 AC: 22713 AN: 41404

American (AMR) AF: 0.630 AC: 9623 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2462 AN: 3468

East Asian (EAS) AF: 0.342 AC: 1767 AN: 5166

South Asian (SAS) AF: 0.576 AC: 2775 AN: 4816

European-Finnish (FIN) AF: 0.592 AC: 6234 AN: 10522

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45304 AN: 67978

Other (OTH) AF: 0.621 AC: 1310 AN: 2108

Alfa AF: 0.648 Hom.: 99646

Bravo AF: 0.612

Asia WGS AF: 0.450 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6505623; hg19: chr18-1125057;