rs4728090

Positions:

• chr7-128190061-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000710955.1(ENSG00000292309):​n.306-15628C>T variant causes a intron, non coding transcript 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: ENST00000710955.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000710955.1	n.306-15628C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.550

Alfa AF: 0.650 Hom.: 61273

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4728090; hg19: chr7-127830114;