rs9610449

Variant names:

• chr22-36215187-T-C
• rs9610449

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 0.289 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.235 AC: 9731 AN: 41454

American (AMR) AF: 0.335 AC: 5122 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3464

East Asian (EAS) AF: 0.0717 AC: 371 AN: 5174

South Asian (SAS) AF: 0.226 AC: 1090 AN: 4818

European-Finnish (FIN) AF: 0.293 AC: 3095 AN: 10560

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.333 AC: 22624 AN: 67950

Other (OTH) AF: 0.311 AC: 657 AN: 2110

Alfa AF: 0.319 Hom.: 3272

Bravo AF: 0.296

Asia WGS AF: 0.178 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.28
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9610449; hg19: chr22-36611233;