5-148913359-C-T

Variant names:

• chr5-148913359-C-T
• rs10875641

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 0.702 in 151,884 control chromosomes in the GnomAD database, including 38,351 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 0.70 (38351 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106443 AN: 151768 Hom.: 38297 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.702 AC: 106553 AN: 151884 Hom.: 38351 Cov.: 31 AF XY: 0.698 AC XY: 51796 AN XY: 74198

African (AFR) AF: 0.861 AC: 35719 AN: 41476

American (AMR) AF: 0.723 AC: 11042 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1880 AN: 3462

East Asian (EAS) AF: 0.730 AC: 3761 AN: 5152

South Asian (SAS) AF: 0.492 AC: 2360 AN: 4800

European-Finnish (FIN) AF: 0.628 AC: 6596 AN: 10510

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43035 AN: 67908

Other (OTH) AF: 0.643 AC: 1352 AN: 2104

Alfa AF: 0.645 Hom.: 23274

Bravo AF: 0.722

Asia WGS AF: 0.643 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs10875641; hg19: chr5-148292922;