4-156430090-T-C

Variant names:

• chr4-156430090-T-C
• rs10517636
• ENST00000778470.1:n.394-3067T>C

Variant summary

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

The ENST00000778470.1(ENSG00000301356):​n.394-3067T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,860 control chromosomes in the GnomAD database, including 14,638 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 0.43 (14638 hom., cov: 31)
• Consequence: ENSG00000301356 ENST00000778470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 1 publications found

Genes affected

ENSG00000301356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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
ENSG00000301356	ENST00000778470.1	n.394-3067T>C		intron_variant	Intron 3 of 4
ENSG00000301356	ENST00000778471.1	n.203-3067T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64754 AN: 151740 Hom.: 14618 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.427 AC: 64819 AN: 151860 Hom.: 14638 Cov.: 31 AF XY: 0.422 AC XY: 31286 AN XY: 74222

African (AFR) AF: 0.557 AC: 23060 AN: 41384

American (AMR) AF: 0.364 AC: 5553 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3470

East Asian (EAS) AF: 0.142 AC: 735 AN: 5172

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4810

European-Finnish (FIN) AF: 0.403 AC: 4248 AN: 10536

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26834 AN: 67928

Other (OTH) AF: 0.414 AC: 874 AN: 2112

Alfa AF: 0.402 Hom.: 52982

Bravo AF: 0.429

Asia WGS AF: 0.242 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.70
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs10517636; hg19: chr4-157351242;