5-73104363-T-C

Position:

• chr5-73104363-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 0.244 in 152,036 control chromosomes in the GnomAD database, including 6,279 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 0.24 (6279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 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: 0.243 AC: 36967 AN: 151918 Hom.: 6257 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.244 AC: 37030 AN: 152036 Hom.: 6279 Cov.: 32 AF XY: 0.242 AC XY: 17981 AN XY: 74322

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.222

Alfa AF: 0.157 Hom.: 2903

Bravo AF: 0.256

Asia WGS AF: 0.262 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs683633; hg19: chr5-72400190;