rs74360883

Variant names:

• chr11-45529203-A-G
• rs74360883
• ENST00000527642.5:n.495+2322T>C

Variant summary

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

The ENST00000527642.5(ENSG00000254746):​n.495+2322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0448 in 152,226 control chromosomes in the GnomAD database, including 370 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 0.045 (370 hom., cov: 32)
• Consequence: ENSG00000254746 ENST00000527642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 1 publications found

Genes affected

ENSG00000254746 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376654	XR_001748204.3	n.711+2322T>C		intron_variant	Intron 4 of 4
LOC105376654	XR_931245.4	n.368+2322T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254746	ENST00000527642.5	n.495+2322T>C		intron_variant	Intron 5 of 5	4
ENSG00000254746	ENST00000533315.5	n.490+2322T>C		intron_variant	Intron 4 of 4	4
ENSG00000254746	ENST00000654281.1	n.724+2322T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0447 AC: 6796 AN: 152108 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00767

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0448 AC: 6817 AN: 152226 Hom.: 370 Cov.: 32 AF XY: 0.0436 AC XY: 3243 AN XY: 74438

African (AFR) AF: 0.128 AC: 5295 AN: 41516

American (AMR) AF: 0.0237 AC: 362 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.00767 AC: 37 AN: 4822

European-Finnish (FIN) AF: 0.0106 AC: 113 AN: 10620

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0127 AC: 867 AN: 68006

Other (OTH) AF: 0.0379 AC: 80 AN: 2112

Alfa AF: 0.0292 Hom.: 58

Bravo AF: 0.0489

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.21
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs74360883; hg19: chr11-45550753;