5-5581435-A-G

Variant names:

• chr5-5581435-A-G
• rs246765
• ENST00000796428.1:n.329+7443A>G

Variant summary

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

The ENST00000796428.1(ENSG00000303674):​n.329+7443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,278 control chromosomes in the GnomAD database, including 62,778 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 0.91 (62778 hom., cov: 32)
• Consequence: ENSG00000303674 ENST00000796428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 7 publications found

Genes affected

ENSG00000303674 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.923 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
ENSG00000303674	ENST00000796428.1	n.329+7443A>G		intron_variant	Intron 1 of 1
ENSG00000303674	ENST00000796429.1	n.296+7443A>G		intron_variant	Intron 1 of 2
ENSG00000303674	ENST00000796430.1	n.245+7443A>G		intron_variant	Intron 1 of 3
ENSG00000303674	ENST00000796431.1	n.329+7443A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.907 AC: 138023 AN: 152160 Hom.: 62725 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.907 AC: 138133 AN: 152278 Hom.: 62778 Cov.: 32 AF XY: 0.904 AC XY: 67306 AN XY: 74446

African (AFR) AF: 0.899 AC: 37361 AN: 41552

American (AMR) AF: 0.849 AC: 12981 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3109 AN: 3468

East Asian (EAS) AF: 0.903 AC: 4677 AN: 5182

South Asian (SAS) AF: 0.855 AC: 4121 AN: 4822

European-Finnish (FIN) AF: 0.919 AC: 9741 AN: 10602

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63179 AN: 68036

Other (OTH) AF: 0.909 AC: 1924 AN: 2116

Alfa AF: 0.918 Hom.: 10396

Bravo AF: 0.907

Asia WGS AF: 0.870 AC: 3029 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	0.32
DANN	Benign	0.18
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs246765; hg19: chr5-5581548;