rs131408

Variant names:

• chr22-23548649-T-C
• rs131408

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 0.49 in 152,018 control chromosomes in the GnomAD database, including 20,536 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 0.49 (20536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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: 0.489 AC: 74330 AN: 151900 Hom.: 20484 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.490 AC: 74443 AN: 152018 Hom.: 20536 Cov.: 32 AF XY: 0.492 AC XY: 36568 AN XY: 74286

African (AFR) AF: 0.750 AC: 31094 AN: 41474

American (AMR) AF: 0.477 AC: 7292 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3468

East Asian (EAS) AF: 0.663 AC: 3427 AN: 5170

South Asian (SAS) AF: 0.448 AC: 2159 AN: 4824

European-Finnish (FIN) AF: 0.407 AC: 4291 AN: 10550

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23540 AN: 67928

Other (OTH) AF: 0.472 AC: 998 AN: 2114

Alfa AF: 0.403 Hom.: 41170

Bravo AF: 0.510

Asia WGS AF: 0.598 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.45
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs131408; hg19: chr22-23890836;