5-130681594-T-C

Variant names:

• chr5-130681594-T-C
• rs4836519
• ENST00000661392.1:n.349-3956A>G

Variant summary

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

The ENST00000661392.1(ENSG00000287390):​n.349-3956A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,506 control chromosomes in the GnomAD database, including 3,095 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 0.19 (3095 hom., cov: 32)
• Consequence: ENSG00000287390 ENST00000661392.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 26 publications found

Genes affected

ENSG00000287390 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.299 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
ENSG00000287390	ENST00000661392.1	n.349-3956A>G		intron_variant	Intron 4 of 5
ENSG00000287390	ENST00000804525.1	n.451-3956A>G		intron_variant	Intron 4 of 4
ENSG00000287390	ENST00000804527.1	n.470-3956A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29041 AN: 151392 Hom.: 3091 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0837

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.192 AC: 29047 AN: 151506 Hom.: 3095 Cov.: 32 AF XY: 0.196 AC XY: 14475 AN XY: 74018

African (AFR) AF: 0.105 AC: 4345 AN: 41390

American (AMR) AF: 0.160 AC: 2435 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3464

East Asian (EAS) AF: 0.215 AC: 1110 AN: 5162

South Asian (SAS) AF: 0.313 AC: 1502 AN: 4806

European-Finnish (FIN) AF: 0.275 AC: 2855 AN: 10398

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15626 AN: 67776

Other (OTH) AF: 0.163 AC: 344 AN: 2108

Alfa AF: 0.214 Hom.: 11337

Bravo AF: 0.174

Asia WGS AF: 0.258 AC: 894 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4836519; hg19: chr5-130017287;