5-53866026-A-T

Variant names:

• chr5-53866026-A-T
• rs10940347

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 0.322 in 152,020 control chromosomes in the GnomAD database, including 8,457 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 0.32 (8457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 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: 0.322 AC: 48886 AN: 151904 Hom.: 8454 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.322 AC: 48915 AN: 152020 Hom.: 8457 Cov.: 32 AF XY: 0.319 AC XY: 23717 AN XY: 74294

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.331

Alfa AF: 0.231 Hom.: 598

Bravo AF: 0.317

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10940347; hg19: chr5-53161856;