5-148821922-A-T

Variant names:

• chr5-148821922-A-T
• rs11958940

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 0.595 in 151,710 control chromosomes in the GnomAD database, including 27,203 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 0.59 (27203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90128 AN: 151592 Hom.: 27185 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.595 AC: 90192 AN: 151710 Hom.: 27203 Cov.: 32 AF XY: 0.602 AC XY: 44636 AN XY: 74138

African (AFR) AF: 0.560 AC: 23141 AN: 41310

American (AMR) AF: 0.707 AC: 10806 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2067 AN: 3462

East Asian (EAS) AF: 0.743 AC: 3839 AN: 5164

South Asian (SAS) AF: 0.738 AC: 3562 AN: 4824

European-Finnish (FIN) AF: 0.630 AC: 6610 AN: 10500

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38147 AN: 67870

Other (OTH) AF: 0.626 AC: 1318 AN: 2104

Alfa AF: 0.431 Hom.: 1121

Bravo AF: 0.596

Asia WGS AF: 0.747 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.60
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs11958940; hg19: chr5-148201485;