rs2224572

Positions:

• chr9-5288707-T-A
• chr9-5288707-T-C

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 0.438 in 152,006 control chromosomes in the GnomAD database, including 14,811 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 0.44 (14811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 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: 0.438 AC: 66481 AN: 151888 Hom.: 14785 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.438 AC: 66551 AN: 152006 Hom.: 14811 Cov.: 32 AF XY: 0.438 AC XY: 32563 AN XY: 74328

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.470

Alfa AF: 0.403 Hom.: 1789

Bravo AF: 0.449

Asia WGS AF: 0.537 AC: 1864 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2224572; hg19: chr9-5288707; COSMIC: COSV60324010;