chr5-50629713-T-C

Position:

• chr5-50629713-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 0.0945 in 152,134 control chromosomes in the GnomAD database, including 943 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 0.094 (943 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.0943 AC: 14329 AN: 152016 Hom.: 927 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.0940

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.0870

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

GnomAD4 genome AF: 0.0945 AC: 14375 AN: 152134 Hom.: 943 Cov.: 32 AF XY: 0.0916 AC XY: 6814 AN XY: 74384

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0719

Gnomad4 ASJ AF: 0.0940

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.0406

Gnomad4 NFE AF: 0.0687

Gnomad4 OTH AF: 0.0861

Alfa AF: 0.0783 Hom.: 132

Bravo AF: 0.100

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6892149; hg19: chr5-49925547;