5-76708421-A-G

Variant names:

• chr5-76708421-A-G
• rs153317
• ENST00000507514.1:n.39+7756T>C

Variant summary

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

The ENST00000507514.1(ENSG00000225407):​n.39+7756T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,962 control chromosomes in the GnomAD database, including 19,167 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 0.49 (19167 hom., cov: 32)
• Consequence: ENSG00000225407 ENST00000507514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 6 publications found

Genes affected

ENSG00000225407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 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
ENSG00000225407	ENST00000507514.1	n.39+7756T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74628 AN: 151844 Hom.: 19133 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.492 AC: 74720 AN: 151962 Hom.: 19167 Cov.: 32 AF XY: 0.493 AC XY: 36653 AN XY: 74276

African (AFR) AF: 0.647 AC: 26793 AN: 41436

American (AMR) AF: 0.436 AC: 6663 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2394 AN: 5168

South Asian (SAS) AF: 0.515 AC: 2481 AN: 4818

European-Finnish (FIN) AF: 0.440 AC: 4635 AN: 10538

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28517 AN: 67956

Other (OTH) AF: 0.466 AC: 980 AN: 2102

Alfa AF: 0.440 Hom.: 15287

Bravo AF: 0.496

Asia WGS AF: 0.499 AC: 1735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.42
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs153317; hg19: chr5-76004246;