rs7494783

Variant names:

• chr15-56029404-T-C
• rs7494783

Variant summary

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

The variant allele was found at a frequency of 0.0781 in 152,250 control chromosomes in the GnomAD database, including 599 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 0.078 (599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 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

Frequencies

GnomAD3 genomes AF: 0.0781 AC: 11882 AN: 152132 Hom.: 598 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.0468

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0781 AC: 11887 AN: 152250 Hom.: 599 Cov.: 32 AF XY: 0.0768 AC XY: 5719 AN XY: 74438

Gnomad4 AFR AF: 0.0194

Gnomad4 AMR AF: 0.0954

Gnomad4 ASJ AF: 0.0423

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.0468

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0982 Hom.: 464

Bravo AF: 0.0750

Asia WGS AF: 0.0550 AC: 192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7494783; hg19: chr15-56321602;