rs4728090

Variant names:

• chr7-128190061-C-T
• rs4728090
• ENST00000710955.1:n.306-15628C>T

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.306-15628C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,154 control chromosomes in the GnomAD database, including 23,637 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 0.51 (23637 hom., cov: 33)
• Consequence: ENSG00000292309 ENST00000710955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 4 publications found

Genes affected

ENSG00000292309 (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 (EAS) allele frequency at 95% confidence interval = 0.679 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
ENSG00000292309	ENST00000710955.1	n.306-15628C>T		intron_variant	Intron 1 of 3
ENSG00000292309	ENST00000765690.1	n.233-15622C>T		intron_variant	Intron 2 of 4
ENSG00000292309	ENST00000765691.1	n.142-15622C>T		intron_variant	Intron 1 of 3
ENSG00000292309	ENST00000765692.1	n.190-11574C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77342 AN: 152036 Hom.: 23639 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.508 AC: 77333 AN: 152154 Hom.: 23637 Cov.: 33 AF XY: 0.507 AC XY: 37694 AN XY: 74358

African (AFR) AF: 0.147 AC: 6118 AN: 41528

American (AMR) AF: 0.533 AC: 8140 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2259 AN: 3470

East Asian (EAS) AF: 0.698 AC: 3608 AN: 5168

South Asian (SAS) AF: 0.550 AC: 2654 AN: 4824

European-Finnish (FIN) AF: 0.614 AC: 6484 AN: 10564

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.677 AC: 46023 AN: 68000

Other (OTH) AF: 0.550 AC: 1160 AN: 2110

Alfa AF: 0.616 Hom.: 78814

Bravo AF: 0.488

Asia WGS AF: 0.548 AC: 1908 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	4.5
DANN	Benign	0.61
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4728090; hg19: chr7-127830114;