4-130053048-C-G

Variant names:

• chr4-130053048-C-G
• rs10518560
• ENST00000839037.1:n.434+19950C>G

Variant summary

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

The ENST00000839037.1(ENSG00000309145):​n.434+19950C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,144 control chromosomes in the GnomAD database, including 2,127 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 0.11 (2127 hom., cov: 33)
• Consequence: ENSG00000309145 ENST00000839037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 0 publications found

Genes affected

ENSG00000309145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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
ENSG00000309145	ENST00000839037.1	n.434+19950C>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16187 AN: 152026 Hom.: 2118 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.0721

Gnomad SAS AF: 0.0463

Gnomad FIN AF: 0.0583

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0874

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

GnomAD4 genome AF: 0.107 AC: 16234 AN: 152144 Hom.: 2127 Cov.: 33 AF XY: 0.106 AC XY: 7855 AN XY: 74394

African (AFR) AF: 0.312 AC: 12918 AN: 41456

American (AMR) AF: 0.0761 AC: 1164 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3470

East Asian (EAS) AF: 0.0724 AC: 375 AN: 5176

South Asian (SAS) AF: 0.0472 AC: 227 AN: 4808

European-Finnish (FIN) AF: 0.0583 AC: 618 AN: 10596

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0104 AC: 706 AN: 68026

Other (OTH) AF: 0.0945 AC: 200 AN: 2116

Alfa AF: 0.0202 Hom.: 38

Bravo AF: 0.116

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.57
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10518560; hg19: chr4-130974203;