ENST00000810670.1:n.452+4334G>A

Variant names:

• chr5-130372657-G-A
• rs7726515
• ENST00000810670.1:n.452+4334G>A

Variant summary

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

The ENST00000810670.1(ENSG00000305378):​n.452+4334G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,974 control chromosomes in the GnomAD database, including 3,085 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 0.20 (3085 hom., cov: 31)
• Consequence: ENSG00000305378 ENST00000810670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 4 publications found

Genes affected

ENSG00000305378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379171	XR_001742880.1	n.999+4334G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305378	ENST00000810670.1	n.452+4334G>A		intron_variant	Intron 3 of 3
ENSG00000305378	ENST00000810671.1	n.467-4021G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29989 AN: 151856 Hom.: 3085 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.197 AC: 29993 AN: 151974 Hom.: 3085 Cov.: 31 AF XY: 0.198 AC XY: 14699 AN XY: 74278

African (AFR) AF: 0.178 AC: 7370 AN: 41474

American (AMR) AF: 0.144 AC: 2193 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 407 AN: 3460

East Asian (EAS) AF: 0.179 AC: 922 AN: 5146

South Asian (SAS) AF: 0.188 AC: 906 AN: 4818

European-Finnish (FIN) AF: 0.255 AC: 2692 AN: 10544

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14965 AN: 67948

Other (OTH) AF: 0.155 AC: 327 AN: 2112

Alfa AF: 0.207 Hom.: 13571

Bravo AF: 0.186

Asia WGS AF: 0.183 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.64
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs7726515; hg19: chr5-129708350;