rs734780

chr15-89021727-T-Cchr15-89021727-T-G

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 0.286 in 152,120 control chromosomes in the GnomAD database, including 10,459 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 0.29 (10459 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43360 AN: 152002 Hom.: 10413 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0862

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.286 AC: 43474 AN: 152120 Hom.: 10459 Cov.: 32 AF XY: 0.290 AC XY: 21561 AN XY: 74372

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.0985

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.0862

Gnomad4 OTH AF: 0.262

Alfa AF: 0.0822 Hom.: 179

Bravo AF: 0.319

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.9
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs734780; hg19: chr15-89564958;