5-10267803-T-C

Variant names:

• chr5-10267803-T-C
• rs2578645

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 0.739 in 151,988 control chromosomes in the GnomAD database, including 43,696 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 0.74 (43696 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 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: 0.739 AC: 112234 AN: 151870 Hom.: 43678 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.739 AC: 112293 AN: 151988 Hom.: 43696 Cov.: 31 AF XY: 0.742 AC XY: 55123 AN XY: 74278

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.769

Alfa AF: 0.774 Hom.: 6904

Bravo AF: 0.727

Asia WGS AF: 0.773 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2578645; hg19: chr5-10267915;