4-155585717-T-C

Variant names:

• chr4-155585717-T-C
• rs716428
• ENST00000730967.1:n.270-6769T>C

Variant summary

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

The ENST00000730967.1(ENSG00000251244):​n.270-6769T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,086 control chromosomes in the GnomAD database, including 21,406 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 0.52 (21406 hom., cov: 32)
• Consequence: ENSG00000251244 ENST00000730967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 9 publications found

Genes affected

ENSG00000251244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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
ENSG00000251244	ENST00000730967.1	n.270-6769T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79769 AN: 151968 Hom.: 21401 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.525 AC: 79817 AN: 152086 Hom.: 21406 Cov.: 32 AF XY: 0.536 AC XY: 39830 AN XY: 74338

African (AFR) AF: 0.429 AC: 17772 AN: 41462

American (AMR) AF: 0.529 AC: 8096 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1781 AN: 3470

East Asian (EAS) AF: 0.745 AC: 3849 AN: 5168

South Asian (SAS) AF: 0.693 AC: 3338 AN: 4816

European-Finnish (FIN) AF: 0.621 AC: 6565 AN: 10568

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36632 AN: 67992

Other (OTH) AF: 0.525 AC: 1109 AN: 2114

Alfa AF: 0.516 Hom.: 9958

Bravo AF: 0.510

Asia WGS AF: 0.676 AC: 2347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.61
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs716428; hg19: chr4-156506869;