rs9610449

Variant names:

• chr22-36215187-T-C
• rs9610449

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 0.289 in 152,018 control chromosomes in the GnomAD database, including 6,722 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 0.29 (6722 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.329 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: 0.290 AC: 43980 AN: 151902 Hom.: 6717 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0712

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.289 AC: 44006 AN: 152018 Hom.: 6722 Cov.: 31 AF XY: 0.285 AC XY: 21146 AN XY: 74286

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0717

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.311

Alfa AF: 0.318 Hom.: 2626

Bravo AF: 0.296

Asia WGS AF: 0.178 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9610449; hg19: chr22-36611233;