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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.440 AC: 18232 AN: 41426

American (AMR) AF: 0.346 AC: 5298 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3468

East Asian (EAS) AF: 0.512 AC: 2636 AN: 5152

South Asian (SAS) AF: 0.386 AC: 1857 AN: 4816

European-Finnish (FIN) AF: 0.335 AC: 3537 AN: 10552

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21460 AN: 67930

Other (OTH) AF: 0.322 AC: 678 AN: 2108

Alfa AF: 0.325 Hom.: 14036

Bravo AF: 0.368

Asia WGS AF: 0.401 AC: 1394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.39
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2338712; hg19: chr22-48827287;