5-111137830-A-T

Variant names:

• chr5-111137830-A-T
• rs417670

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 0.684 in 152,138 control chromosomes in the GnomAD database, including 36,317 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 0.68 (36317 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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: 0.684 AC: 103940 AN: 152020 Hom.: 36289 Cov.: 33

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.684 AC: 104026 AN: 152138 Hom.: 36317 Cov.: 33 AF XY: 0.694 AC XY: 51616 AN XY: 74390

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.668

Alfa AF: 0.649 Hom.: 3836

Bravo AF: 0.677

Asia WGS AF: 0.873 AC: 3037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs417670; hg19: chr5-110473528;