rs4869419

Variant names:

• chr5-93231833-A-G
• rs4869419
• ENST00000762928.1:n.272+20287T>C

Variant summary

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

The ENST00000762928.1(ENSG00000251361):​n.272+20287T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 152,064 control chromosomes in the GnomAD database, including 504 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 0.069 (504 hom., cov: 32)
• Consequence: ENSG00000251361 ENST00000762928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 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.272+20287T>C		intron_variant	Intron 1 of 5
ENSG00000251361	ENST00000762929.1	n.91+20414T>C		intron_variant	Intron 1 of 5
ENSG00000251361	ENST00000762930.1	n.81+28620T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0686 AC: 10427 AN: 151946 Hom.: 500 Cov.: 32

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0410

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0550

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0686 AC: 10434 AN: 152064 Hom.: 504 Cov.: 32 AF XY: 0.0707 AC XY: 5255 AN XY: 74350

African (AFR) AF: 0.0350 AC: 1451 AN: 41512

American (AMR) AF: 0.127 AC: 1938 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0410 AC: 142 AN: 3464

East Asian (EAS) AF: 0.140 AC: 722 AN: 5172

South Asian (SAS) AF: 0.166 AC: 798 AN: 4820

European-Finnish (FIN) AF: 0.0550 AC: 582 AN: 10574

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0675 AC: 4590 AN: 67978

Other (OTH) AF: 0.0674 AC: 142 AN: 2108

Alfa AF: 0.0689 Hom.: 1344

Bravo AF: 0.0684

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.87
DANN	Benign	0.84
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4869419; hg19: chr5-92567539;