4-11318787-T-C

Variant names:

• chr4-11318787-T-C
• rs17383790
• ENST00000835362.1:n.133+4847T>C

Variant summary

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

The ENST00000835362.1(ENSG00000308608):​n.133+4847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,128 control chromosomes in the GnomAD database, including 2,097 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 0.16 (2097 hom., cov: 32)
• Consequence: ENSG00000308608 ENST00000835362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 5 publications found

Genes affected

ENSG00000308608 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835362.1. 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
	ENSG00000308608	ENST00000835362.1		n.133+4847T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24263 AN: 152010 Hom.: 2087 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.160 AC: 24299 AN: 152128 Hom.: 2097 Cov.: 32 AF XY: 0.161 AC XY: 11974 AN XY: 74350

African (AFR) AF: 0.128 AC: 5325 AN: 41494

American (AMR) AF: 0.116 AC: 1781 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3472

East Asian (EAS) AF: 0.106 AC: 549 AN: 5182

South Asian (SAS) AF: 0.236 AC: 1136 AN: 4814

European-Finnish (FIN) AF: 0.226 AC: 2384 AN: 10566

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12183 AN: 67994

Other (OTH) AF: 0.147 AC: 310 AN: 2112

Alfa AF: 0.166 Hom.: 6828

Bravo AF: 0.147

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.73
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs17383790; hg19: chr4-11320411;