5-93128710-T-C

Variant names:

• chr5-93128710-T-C
• rs12519773
• ENST00000762928.1:n.449+21116A>G

Variant summary

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

The ENST00000762928.1(ENSG00000251361):​n.449+21116A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,908 control chromosomes in the GnomAD database, including 23,987 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 (23987 hom., cov: 32)
• Consequence: ENSG00000251361 ENST00000762928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 8 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 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.449+21116A>G		intron_variant	Intron 3 of 5
ENSG00000251361	ENST00000762929.1	n.268+21116A>G		intron_variant	Intron 3 of 5
ENSG00000251361	ENST00000762930.1	n.258+21116A>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83266 AN: 151790 Hom.: 23946 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.549 AC: 83370 AN: 151908 Hom.: 23987 Cov.: 32 AF XY: 0.553 AC XY: 41067 AN XY: 74220

African (AFR) AF: 0.693 AC: 28708 AN: 41448

American (AMR) AF: 0.601 AC: 9162 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1014 AN: 3464

East Asian (EAS) AF: 0.699 AC: 3613 AN: 5170

South Asian (SAS) AF: 0.527 AC: 2534 AN: 4812

European-Finnish (FIN) AF: 0.517 AC: 5451 AN: 10534

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31260 AN: 67922

Other (OTH) AF: 0.507 AC: 1070 AN: 2112

Alfa AF: 0.489 Hom.: 6630

Bravo AF: 0.565

Asia WGS AF: 0.646 AC: 2243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.23
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12519773; hg19: chr5-92464416;