5-34389754-T-C

Position:

• chr5-34389754-T-C

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 0.975 in 146,854 control chromosomes in the GnomAD database, including 69,856 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 0.97 (69856 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 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: 0.975 AC: 143050 AN: 146742 Hom.: 69816 Cov.: 23

Gnomad AFR AF: 0.963

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.981

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

GnomAD4 genome AF: 0.975 AC: 143141 AN: 146854 Hom.: 69856 Cov.: 23 AF XY: 0.972 AC XY: 69378 AN XY: 71360

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.996

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.997

Gnomad4 OTH AF: 0.981

Alfa AF: 0.991 Hom.: 60866

Bravo AF: 0.969

Asia WGS AF: 0.913 AC: 3162 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.2
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: rs1440423; hg19: chr5-34389859;