chr4-117725752-A-G

Variant names:

• chr4-117725752-A-G
• rs11098403
• ENST00000755294.1:n.275+23561T>C

Variant summary

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

The ENST00000755294.1(ENSG00000288921):​n.275+23561T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,012 control chromosomes in the GnomAD database, including 4,950 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 0.25 (4950 hom., cov: 30)
• Consequence: ENSG00000288921 ENST00000755294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 23 publications found

Genes affected

ENSG00000288921 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755294.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288921	ENST00000755294.1		n.275+23561T>C		intron	N/A
	ENSG00000288921	ENST00000755295.1		n.350+23462T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38085 AN: 151894 Hom.: 4951 Cov.: 30

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.251 AC: 38093 AN: 152012 Hom.: 4950 Cov.: 30 AF XY: 0.243 AC XY: 18047 AN XY: 74278

African (AFR) AF: 0.243 AC: 10079 AN: 41456

American (AMR) AF: 0.229 AC: 3489 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1417 AN: 3470

East Asian (EAS) AF: 0.146 AC: 750 AN: 5150

South Asian (SAS) AF: 0.206 AC: 995 AN: 4824

European-Finnish (FIN) AF: 0.164 AC: 1735 AN: 10578

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18487 AN: 67962

Other (OTH) AF: 0.296 AC: 626 AN: 2112

Alfa AF: 0.270 Hom.: 26131

Bravo AF: 0.257

Asia WGS AF: 0.188 AC: 655 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.40
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs11098403; hg19: chr4-118646907;