rs11585798

Variant names:

• chr1-159668225-T-A
• rs11585798
• ENST00000751816.1:n.107+7536T>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.107+7536T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,180 control chromosomes in the GnomAD database, including 1,357 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 0.11 (1357 hom., cov: 34)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489
• Publications: 3 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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
ENSG00000297913	ENST00000751816.1	n.107+7536T>A		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.109+7536T>A		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.62+7536T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17322 AN: 152062 Hom.: 1358 Cov.: 34

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.114 AC: 17328 AN: 152180 Hom.: 1357 Cov.: 34 AF XY: 0.119 AC XY: 8873 AN XY: 74406

African (AFR) AF: 0.0221 AC: 920 AN: 41574

American (AMR) AF: 0.153 AC: 2333 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1963 AN: 5140

South Asian (SAS) AF: 0.109 AC: 524 AN: 4816

European-Finnish (FIN) AF: 0.222 AC: 2350 AN: 10584

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8513 AN: 68000

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.113 Hom.: 52

Asia WGS AF: 0.240 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	6.9
DANN	Benign	0.74
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs11585798; hg19: chr1-159638015;