rs721905

Variant names:

• chr9-8159670-T-C
• rs721905

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 0.384 in 152,148 control chromosomes in the GnomAD database, including 12,334 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 0.38 (12334 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.951
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 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: 0.384 AC: 58409 AN: 152030 Hom.: 12335 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.384 AC: 58444 AN: 152148 Hom.: 12334 Cov.: 33 AF XY: 0.387 AC XY: 28752 AN XY: 74374

African (AFR) AF: 0.210 AC: 8727 AN: 41530

American (AMR) AF: 0.395 AC: 6034 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2820 AN: 5178

South Asian (SAS) AF: 0.550 AC: 2649 AN: 4816

European-Finnish (FIN) AF: 0.392 AC: 4147 AN: 10574

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31205 AN: 67984

Other (OTH) AF: 0.417 AC: 879 AN: 2110

Alfa AF: 0.439 Hom.: 10145

Bravo AF: 0.374

Asia WGS AF: 0.511 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs721905; hg19: chr9-8159670;