rs5750116

Variant names:

• chr22-35568675-C-T
• rs5750116
• ENST00000802901.1:n.400-4884G>A

Variant summary

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

The ENST00000802901.1(ENSG00000304364):​n.400-4884G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,172 control chromosomes in the GnomAD database, including 30,831 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 0.63 (30831 hom., cov: 34)
• Consequence: ENSG00000304364 ENST00000802901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910
• Publications: 5 publications found

Genes affected

ENSG00000304364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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
ENSG00000304364	ENST00000802901.1	n.400-4884G>A		intron_variant	Intron 2 of 2
ENSG00000304364	ENST00000802902.1	n.344-4884G>A		intron_variant	Intron 2 of 2
ENSG00000304364	ENST00000802903.1	n.186-4884G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95712 AN: 152054 Hom.: 30830 Cov.: 34

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.629 AC: 95729 AN: 152172 Hom.: 30831 Cov.: 34 AF XY: 0.630 AC XY: 46859 AN XY: 74388

African (AFR) AF: 0.493 AC: 20478 AN: 41508

American (AMR) AF: 0.622 AC: 9504 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2304 AN: 3468

East Asian (EAS) AF: 0.547 AC: 2830 AN: 5174

South Asian (SAS) AF: 0.563 AC: 2715 AN: 4824

European-Finnish (FIN) AF: 0.752 AC: 7976 AN: 10602

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.702 AC: 47751 AN: 67988

Other (OTH) AF: 0.628 AC: 1328 AN: 2114

Alfa AF: 0.667 Hom.: 63259

Bravo AF: 0.613

Asia WGS AF: 0.529 AC: 1837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs5750116; hg19: chr22-35964722;