chr4-117715115-A-G

Variant names:

• chr4-117715115-A-G
• rs1380376
• ENST00000755294.1:n.275+34198T>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+34198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,074 control chromosomes in the GnomAD database, including 1,479 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 0.13 (1479 hom., cov: 32)
• Consequence: ENSG00000288921 ENST00000755294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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
ENSG00000288921	ENST00000755294.1	n.275+34198T>C		intron_variant	Intron 3 of 5
ENSG00000288921	ENST00000755295.1	n.350+34099T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19618 AN: 151956 Hom.: 1478 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0451

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.129 AC: 19637 AN: 152074 Hom.: 1479 Cov.: 32 AF XY: 0.125 AC XY: 9304 AN XY: 74362

African (AFR) AF: 0.206 AC: 8546 AN: 41506

American (AMR) AF: 0.108 AC: 1644 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.144 AC: 744 AN: 5174

South Asian (SAS) AF: 0.0455 AC: 220 AN: 4834

European-Finnish (FIN) AF: 0.0556 AC: 585 AN: 10530

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6916 AN: 67968

Other (OTH) AF: 0.146 AC: 309 AN: 2110

Alfa AF: 0.106 Hom.: 531

Bravo AF: 0.139

Asia WGS AF: 0.129 AC: 448 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.89
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1380376; hg19: chr4-118636270;