rs9920771

Variant names:

• chr15-72998314-C-T
• rs9920771

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.115 in 152,046 control chromosomes in the GnomAD database, including 2,046 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 0.12 (2046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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: 0.115 AC: 17437 AN: 151928 Hom.: 2039 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.0539

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0537

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.115 AC: 17491 AN: 152046 Hom.: 2046 Cov.: 32 AF XY: 0.113 AC XY: 8364 AN XY: 74324

African (AFR) AF: 0.302 AC: 12505 AN: 41402

American (AMR) AF: 0.0542 AC: 829 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3468

East Asian (EAS) AF: 0.0536 AC: 278 AN: 5182

South Asian (SAS) AF: 0.0383 AC: 185 AN: 4826

European-Finnish (FIN) AF: 0.0537 AC: 568 AN: 10568

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0396 AC: 2694 AN: 68004

Other (OTH) AF: 0.0989 AC: 208 AN: 2104

Alfa AF: 0.0861 Hom.: 215

Bravo AF: 0.124

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs9920771; hg19: chr15-73290655;