5-44702405-T-C

Variant names:

• chr5-44702405-T-C
• rs920329

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 0.481 in 151,532 control chromosomes in the GnomAD database, including 18,374 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 0.48 (18374 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.481 AC: 72806 AN: 151414 Hom.: 18322 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.481 AC: 72910 AN: 151532 Hom.: 18374 Cov.: 32 AF XY: 0.485 AC XY: 35924 AN XY: 74058

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.464

Alfa AF: 0.293 Hom.: 708

Bravo AF: 0.496

Asia WGS AF: 0.574 AC: 1993 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	0.47
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs920329; hg19: chr5-44702507; COSMIC: COSV73949921;