rs1818116

Variant names:

• chr5-32841828-A-G
• rs1818116
• ENST00000841800.1:n.496-30733T>C

Variant summary

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

The ENST00000841800.1(ENSG00000250697):​n.496-30733T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,074 control chromosomes in the GnomAD database, including 10,869 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 0.38 (10869 hom., cov: 32)
• Consequence: ENSG00000250697 ENST00000841800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 5 publications found

Genes affected

ENSG00000250697 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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
ENSG00000250697	ENST00000841800.1	n.496-30733T>C		intron_variant	Intron 3 of 3
ENSG00000309532	ENST00000841854.1	n.230-8326A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57090 AN: 151956 Hom.: 10874 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.376 AC: 57113 AN: 152074 Hom.: 10869 Cov.: 32 AF XY: 0.372 AC XY: 27665 AN XY: 74332

African (AFR) AF: 0.347 AC: 14397 AN: 41474

American (AMR) AF: 0.335 AC: 5112 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2319 AN: 5158

South Asian (SAS) AF: 0.318 AC: 1534 AN: 4818

European-Finnish (FIN) AF: 0.378 AC: 4004 AN: 10580

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26963 AN: 67974

Other (OTH) AF: 0.414 AC: 875 AN: 2114

Alfa AF: 0.390 Hom.: 19931

Bravo AF: 0.373

Asia WGS AF: 0.365 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.62
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1818116; hg19: chr5-32841934;