chr5-50629713-T-C

Variant names:

• chr5-50629713-T-C
• rs6892149

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;