5-93114943-A-G

Variant names:

• chr5-93114943-A-G
• rs959922
• ENST00000762928.1:n.450-24506T>C

Variant summary

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

The ENST00000762928.1(ENSG00000251361):​n.450-24506T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,732 control chromosomes in the GnomAD database, including 24,041 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 0.55 (24041 hom., cov: 31)
• Consequence: ENSG00000251361 ENST00000762928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 5 publications found

Genes affected

ENSG00000251361 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 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
ENSG00000251361	ENST00000762928.1	n.450-24506T>C		intron_variant	Intron 3 of 5
ENSG00000251361	ENST00000762929.1	n.269-24506T>C		intron_variant	Intron 3 of 5
ENSG00000251361	ENST00000762930.1	n.258+34883T>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83317 AN: 151614 Hom.: 24000 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.550 AC: 83421 AN: 151732 Hom.: 24041 Cov.: 31 AF XY: 0.555 AC XY: 41115 AN XY: 74140

African (AFR) AF: 0.694 AC: 28732 AN: 41430

American (AMR) AF: 0.602 AC: 9140 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1014 AN: 3456

East Asian (EAS) AF: 0.713 AC: 3656 AN: 5128

South Asian (SAS) AF: 0.529 AC: 2550 AN: 4824

European-Finnish (FIN) AF: 0.518 AC: 5460 AN: 10548

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31232 AN: 67850

Other (OTH) AF: 0.509 AC: 1075 AN: 2110

Alfa AF: 0.525 Hom.: 3698

Bravo AF: 0.566

Asia WGS AF: 0.661 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.8
DANN	Benign	0.69
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs959922; hg19: chr5-92450649;