4-189202164-C-T

Variant names:

• chr4-189202164-C-T
• rs7665939
• ENST00000514966.1:n.178-2479C>T

Variant summary

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

The ENST00000514966.1(ENSG00000251310):​n.178-2479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.083 in 152,208 control chromosomes in the GnomAD database, including 586 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 0.083 (586 hom., cov: 33)
• Consequence: ENSG00000251310 ENST00000514966.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 2 publications found

Genes affected

ENSG00000251310 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 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
ENSG00000251310	ENST00000514966.1	n.178-2479C>T		intron_variant	Intron 1 of 1	2
ENSG00000251310	ENST00000796163.1	n.118+1990C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12604 AN: 152090 Hom.: 584 Cov.: 33

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.00521

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0830 AC: 12628 AN: 152208 Hom.: 586 Cov.: 33 AF XY: 0.0804 AC XY: 5980 AN XY: 74418

African (AFR) AF: 0.0576 AC: 2394 AN: 41534

American (AMR) AF: 0.0974 AC: 1489 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0729 AC: 253 AN: 3472

East Asian (EAS) AF: 0.00522 AC: 27 AN: 5168

South Asian (SAS) AF: 0.0434 AC: 209 AN: 4818

European-Finnish (FIN) AF: 0.0670 AC: 711 AN: 10610

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7206 AN: 68004

Other (OTH) AF: 0.104 AC: 220 AN: 2110

Alfa AF: 0.0946 Hom.: 1528

Bravo AF: 0.0852

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.82
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7665939; hg19: chr4-190123318;