chr4-117717418-T-G

Variant names:

• chr4-117717418-T-G
• rs1459544
• ENST00000755294.1:n.275+31895A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000755294.1(ENSG00000288921):​n.275+31895A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,170 control chromosomes in the GnomAD database, including 2,237 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 0.15 (2237 hom., cov: 32)
• Consequence: ENSG00000288921 ENST00000755294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570
• Publications: 2 publications found

Genes affected

ENSG00000288921 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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+31895A>C		intron_variant	Intron 3 of 5
ENSG00000288921	ENST00000755295.1	n.350+31796A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22812 AN: 152052 Hom.: 2234 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0565

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.150 AC: 22848 AN: 152170 Hom.: 2237 Cov.: 32 AF XY: 0.145 AC XY: 10811 AN XY: 74398

African (AFR) AF: 0.277 AC: 11507 AN: 41526

American (AMR) AF: 0.116 AC: 1780 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3468

East Asian (EAS) AF: 0.145 AC: 750 AN: 5186

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4830

European-Finnish (FIN) AF: 0.0565 AC: 599 AN: 10602

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6965 AN: 67952

Other (OTH) AF: 0.162 AC: 342 AN: 2114

Alfa AF: 0.112 Hom.: 568

Bravo AF: 0.163

Asia WGS AF: 0.134 AC: 465 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1459544; hg19: chr4-118638573;