rs12159761

Positions:

• chr22-38876636-C-G

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 0.198 in 152,018 control chromosomes in the GnomAD database, including 9,475 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 0.20 (9475 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29976 AN: 151900 Hom.: 9432 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00728

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.198 AC: 30077 AN: 152018 Hom.: 9475 Cov.: 31 AF XY: 0.191 AC XY: 14172 AN XY: 74302

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00666

Gnomad4 FIN AF: 0.00151

Gnomad4 NFE AF: 0.0120

Gnomad4 OTH AF: 0.136

Alfa AF: 0.121 Hom.: 689

Bravo AF: 0.225

Asia WGS AF: 0.0540 AC: 188 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	1.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12159761; hg19: chr22-39272641;