5-5609582-C-A

Variant names:

• chr5-5609582-C-A
• rs378932
• ENST00000796378.1:n.196+4746G>T

Variant summary

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

The ENST00000796378.1(ENSG00000303660):​n.196+4746G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,072 control chromosomes in the GnomAD database, including 37,776 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 0.70 (37776 hom., cov: 32)
• Consequence: ENSG00000303660 ENST00000796378.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 6 publications found

Genes affected

ENSG00000303660 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.13).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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
ENSG00000303660	ENST00000796378.1	n.196+4746G>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106663 AN: 151954 Hom.: 37749 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.702 AC: 106737 AN: 152072 Hom.: 37776 Cov.: 32 AF XY: 0.709 AC XY: 52720 AN XY: 74314

African (AFR) AF: 0.659 AC: 27300 AN: 41440

American (AMR) AF: 0.751 AC: 11479 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2295 AN: 3470

East Asian (EAS) AF: 0.959 AC: 4968 AN: 5178

South Asian (SAS) AF: 0.733 AC: 3532 AN: 4820

European-Finnish (FIN) AF: 0.735 AC: 7765 AN: 10568

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46996 AN: 68002

Other (OTH) AF: 0.681 AC: 1436 AN: 2108

Alfa AF: 0.697 Hom.: 49727

Bravo AF: 0.701

Asia WGS AF: 0.845 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.34
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs378932; hg19: chr5-5609695;