chr5-130372657-G-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810670.1. 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
	ENSG00000305378	ENST00000810670.1		n.452+4334G>A		intron	N/A
	ENSG00000305378	ENST00000810671.1		n.467-4021G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7726515;

hg19: chr5-129708350;