rs1353649

Variant names:

• chr11-20232053-A-G
• rs1353649
• ENST00000725917.1:n.616+8148A>G

Variant summary

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

The ENST00000725917.1(ENSG00000294773):​n.616+8148A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,658 control chromosomes in the GnomAD database, including 36,443 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 0.69 (36443 hom., cov: 30)
• Consequence: ENSG00000294773 ENST00000725917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 10 publications found

Genes affected

ENSG00000294773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 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
ENSG00000294773	ENST00000725917.1	n.616+8148A>G		intron_variant	Intron 5 of 5
ENSG00000294773	ENST00000725918.1	n.178+13093A>G		intron_variant	Intron 2 of 2
ENSG00000294773	ENST00000725920.1	n.345-3259A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103879 AN: 151540 Hom.: 36428 Cov.: 30

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.685 AC: 103930 AN: 151658 Hom.: 36443 Cov.: 30 AF XY: 0.689 AC XY: 51013 AN XY: 74088

African (AFR) AF: 0.581 AC: 23906 AN: 41158

American (AMR) AF: 0.659 AC: 10060 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2350 AN: 3472

East Asian (EAS) AF: 0.449 AC: 2312 AN: 5148

South Asian (SAS) AF: 0.849 AC: 4090 AN: 4816

European-Finnish (FIN) AF: 0.764 AC: 8041 AN: 10524

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50794 AN: 67970

Other (OTH) AF: 0.686 AC: 1443 AN: 2102

Alfa AF: 0.721 Hom.: 101898

Bravo AF: 0.665

Asia WGS AF: 0.685 AC: 2378 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.94
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1353649; hg19: chr11-20253599;