rs11665625

Variant names:

• chr18-900331-G-A
• rs11665625
• ENST00000582554.2:n.179-5636C>T

Variant summary

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

The ENST00000582554.2(ENSG00000265179):​n.179-5636C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,000 control chromosomes in the GnomAD database, including 21,005 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 0.52 (21005 hom., cov: 31)
• Consequence: ENSG00000265179 ENST00000582554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 3 publications found

Genes affected

ENSG00000265179 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 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
ENSG00000265179	ENST00000582554.2	n.179-5636C>T		intron_variant	Intron 1 of 1	5
ENSG00000265179	ENST00000717225.1	n.261+5132C>T		intron_variant	Intron 1 of 1
ENSG00000265179	ENST00000717226.1	n.340+3818C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78612 AN: 151882 Hom.: 20987 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.518 AC: 78664 AN: 152000 Hom.: 21005 Cov.: 31 AF XY: 0.517 AC XY: 38421 AN XY: 74302

African (AFR) AF: 0.664 AC: 27523 AN: 41436

American (AMR) AF: 0.518 AC: 7915 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1761 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2041 AN: 5180

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4812

European-Finnish (FIN) AF: 0.487 AC: 5136 AN: 10554

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30576 AN: 67968

Other (OTH) AF: 0.512 AC: 1078 AN: 2104

Alfa AF: 0.487 Hom.: 9196

Bravo AF: 0.529

Asia WGS AF: 0.428 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.21
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs11665625; hg19: chr18-900332;