chr9-5288707-T-A

Variant names:

• chr9-5288707-T-A
• rs2224572

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 0.438 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.480 AC: 19908 AN: 41466

American (AMR) AF: 0.479 AC: 7320 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1653 AN: 3468

East Asian (EAS) AF: 0.536 AC: 2774 AN: 5174

South Asian (SAS) AF: 0.493 AC: 2378 AN: 4822

European-Finnish (FIN) AF: 0.355 AC: 3748 AN: 10562

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27227 AN: 67926

Other (OTH) AF: 0.470 AC: 993 AN: 2114

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
PhyloP100		0.16

Splicing

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

Other links and lift over

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