4-132843587-C-T

Variant names:

• chr4-132843587-C-T
• rs10518621
• ENST00000509628.1:n.165-6393G>A

Variant summary

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

The ENST00000509628.1(ENSG00000251488):​n.165-6393G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,994 control chromosomes in the GnomAD database, including 4,388 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 0.22 (4388 hom., cov: 33)
• Consequence: ENSG00000251488 ENST00000509628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 1 publications found

Genes affected

ENSG00000251488 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 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
ENSG00000251488	ENST00000509628.1	n.165-6393G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32961 AN: 151876 Hom.: 4366 Cov.: 33

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.217 AC: 33036 AN: 151994 Hom.: 4388 Cov.: 33 AF XY: 0.223 AC XY: 16545 AN XY: 74292

African (AFR) AF: 0.310 AC: 12870 AN: 41458

American (AMR) AF: 0.208 AC: 3176 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3468

East Asian (EAS) AF: 0.600 AC: 3095 AN: 5162

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1966 AN: 10552

Middle Eastern (MID) AF: 0.183 AC: 53 AN: 290

European-Non Finnish (NFE) AF: 0.139 AC: 9432 AN: 67954

Other (OTH) AF: 0.215 AC: 454 AN: 2108

Alfa AF: 0.168 Hom.: 7368

Bravo AF: 0.224

Asia WGS AF: 0.417 AC: 1449 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.25
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10518621; hg19: chr4-133764742;