rs9616496

Variant names:

• chr22-49201318-T-C
• rs9616496

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 0.396 in 152,108 control chromosomes in the GnomAD database, including 12,726 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 0.40 (12726 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 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: 0.396 AC: 60241 AN: 151988 Hom.: 12717 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.396 AC: 60268 AN: 152108 Hom.: 12726 Cov.: 33 AF XY: 0.384 AC XY: 28525 AN XY: 74364

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.0914

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.393

Alfa AF: 0.387 Hom.: 1490

Bravo AF: 0.409

Asia WGS AF: 0.179 AC: 625 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	0.12
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9616496; hg19: chr22-49597244;