rs590299

Positions:

• chr9-27601572-C-A
• chr9-27601572-C-T

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 0.608 in 152,074 control chromosomes in the GnomAD database, including 28,830 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 0.61 (28830 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 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: 0.608 AC: 92382 AN: 151956 Hom.: 28797 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.608 AC: 92467 AN: 152074 Hom.: 28830 Cov.: 32 AF XY: 0.606 AC XY: 45020 AN XY: 74340

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.592

Alfa AF: 0.538 Hom.: 2157

Bravo AF: 0.605

Asia WGS AF: 0.496 AC: 1726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.10
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs590299; hg19: chr9-27601570; COSMIC: COSV60347047;