5-39478674-T-C

Position:

• chr5-39478674-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 0.0473 in 151,546 control chromosomes in the GnomAD database, including 192 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 0.047 (192 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890

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 (AFR) allele frequency at 95% confidence interval = 0.0673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 7163 AN: 151434 Hom.: 192 Cov.: 31

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0406

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0492

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0432

Gnomad OTH AF: 0.0422

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

GnomAD4 genome AF: 0.0473 AC: 7169 AN: 151546 Hom.: 192 Cov.: 31 AF XY: 0.0461 AC XY: 3416 AN XY: 74076

Gnomad4 AFR AF: 0.0694

Gnomad4 AMR AF: 0.0405

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.0277

Gnomad4 NFE AF: 0.0433

Gnomad4 OTH AF: 0.0418

Alfa AF: 0.0476 Hom.: 18

Bravo AF: 0.0482

Asia WGS AF: 0.0220 AC: 76 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491480; hg19: chr5-39478776;