5-1297803-T-C

Position:

• chr5-1297803-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 0.88 in 152,118 control chromosomes in the GnomAD database, including 59,149 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 0.88 (59149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

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 = 0.941 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: 0.880 AC: 133775 AN: 152000 Hom.: 59082 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.880 AC: 133903 AN: 152118 Hom.: 59149 Cov.: 32 AF XY: 0.879 AC XY: 65403 AN XY: 74366

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.852

Gnomad4 OTH AF: 0.847

Alfa AF: 0.864 Hom.: 7081

Bravo AF: 0.886

Asia WGS AF: 0.908 AC: 3159 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	1.5
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7449190; hg19: chr5-1297918;