rs2338712

chr22-48431475-G-Achr22-48431475-G-C

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 0.363 in 151,950 control chromosomes in the GnomAD database, including 10,225 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 0.36 (10225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 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: 0.363 AC: 55095 AN: 151832 Hom.: 10214 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.363 AC: 55156 AN: 151950 Hom.: 10225 Cov.: 32 AF XY: 0.364 AC XY: 27005 AN XY: 74256

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.322

Alfa AF: 0.321 Hom.: 10763

Bravo AF: 0.368

Asia WGS AF: 0.401 AC: 1394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.0
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2338712; hg19: chr22-48827287;