chr5-148821692-C-A

Variant names:

• chr5-148821692-C-A
• rs11168066

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 151,992 control chromosomes in the GnomAD database, including 27,364 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 0.60 (27364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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: 0.596 AC: 90441 AN: 151874 Hom.: 27346 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.595 AC: 90505 AN: 151992 Hom.: 27364 Cov.: 32 AF XY: 0.603 AC XY: 44809 AN XY: 74284

African (AFR) AF: 0.561 AC: 23249 AN: 41436

American (AMR) AF: 0.708 AC: 10819 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2075 AN: 3470

East Asian (EAS) AF: 0.745 AC: 3847 AN: 5164

South Asian (SAS) AF: 0.738 AC: 3557 AN: 4820

European-Finnish (FIN) AF: 0.633 AC: 6670 AN: 10530

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38262 AN: 67980

Other (OTH) AF: 0.628 AC: 1320 AN: 2102

Alfa AF: 0.591 Hom.: 4703

Bravo AF: 0.596

Asia WGS AF: 0.747 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.43
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11168066; hg19: chr5-148201255;