rs2338712

Variant names:

• chr22-48431475-G-A
• rs2338712

Your query was ambiguous. Multiple possible variants found:

• chr22-48431475-G-A
• chr22-48431475-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;