chr5-76714881-C-T

Variant names:

• chr5-76714881-C-T
• rs32934
• ENST00000507514.1:n.39+1296G>A

Variant summary

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

The ENST00000507514.1(ENSG00000225407):​n.39+1296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0722 in 152,306 control chromosomes in the GnomAD database, including 729 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 0.072 (729 hom., cov: 33)
• Consequence: ENSG00000225407 ENST00000507514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 13 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507514.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225407	ENST00000507514.1	TSL:3	n.39+1296G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0721 AC: 10980 AN: 152188 Hom.: 727 Cov.: 33

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0722 AC: 10989 AN: 152306 Hom.: 729 Cov.: 33 AF XY: 0.0751 AC XY: 5596 AN XY: 74476

African (AFR) AF: 0.0528 AC: 2197 AN: 41582

American (AMR) AF: 0.0691 AC: 1058 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 131 AN: 3472

East Asian (EAS) AF: 0.408 AC: 2101 AN: 5154

South Asian (SAS) AF: 0.0495 AC: 239 AN: 4830

European-Finnish (FIN) AF: 0.0772 AC: 820 AN: 10626

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0622 AC: 4233 AN: 68016

Other (OTH) AF: 0.0781 AC: 165 AN: 2114

Alfa AF: 0.0610 Hom.: 171

Bravo AF: 0.0751

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.7
DANN	Benign	0.86
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs32934; hg19: chr5-76010706;