5-148913359-C-T

Variant names:

• chr5-148913359-C-T
• rs10875641

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.701 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

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.643

Alfa AF: 0.636 Hom.: 15716

Bravo AF: 0.722

Asia WGS AF: 0.643 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10875641; hg19: chr5-148292922;