rs734780

Variant names:

• chr15-89021727-T-C
• rs734780

Your query was ambiguous. Multiple possible variants found:

• chr15-89021727-T-C
• chr15-89021727-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.629 AC: 26065 AN: 41470

American (AMR) AF: 0.355 AC: 5427 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 342 AN: 3472

East Asian (EAS) AF: 0.456 AC: 2357 AN: 5174

South Asian (SAS) AF: 0.118 AC: 569 AN: 4822

European-Finnish (FIN) AF: 0.207 AC: 2189 AN: 10592

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0862 AC: 5860 AN: 67990

Other (OTH) AF: 0.262 AC: 553 AN: 2110

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs734780; hg19: chr15-89564958;