rs738807

Positions:

• chr22-23892058-C-T

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 0.14 in 152,194 control chromosomes in the GnomAD database, including 1,697 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 0.14 (1697 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21359 AN: 152076 Hom.: 1692 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.140 AC: 21379 AN: 152194 Hom.: 1697 Cov.: 33 AF XY: 0.146 AC XY: 10838 AN XY: 74404

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.118

Alfa AF: 0.135 Hom.: 898

Bravo AF: 0.136

Asia WGS AF: 0.177 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs738807; hg19: chr22-24234245;