5-141027409-A-T

Position:

• chr5-141027409-A-T

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 0.126 in 152,180 control chromosomes in the GnomAD database, including 1,448 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 0.13 (1448 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19097 AN: 152062 Hom.: 1446 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0753

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.126 AC: 19129 AN: 152180 Hom.: 1448 Cov.: 32 AF XY: 0.124 AC XY: 9214 AN XY: 74418

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0909

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0754

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0792

Gnomad4 NFE AF: 0.0924

Gnomad4 OTH AF: 0.116

Alfa AF: 0.112 Hom.: 135

Bravo AF: 0.128

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.4
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6876364; hg19: chr5-140406994;