rs2104543

Variant names:

• chr10-94670214-C-T
• rs2104543

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 0.25 in 152,006 control chromosomes in the GnomAD database, including 5,030 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 0.25 (5030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 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: 0.250 AC: 38020 AN: 151888 Hom.: 5024 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.250 AC: 38045 AN: 152006 Hom.: 5030 Cov.: 32 AF XY: 0.254 AC XY: 18884 AN XY: 74280

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.236

Alfa AF: 0.228 Hom.: 5401

Bravo AF: 0.244

Asia WGS AF: 0.391 AC: 1361 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	0.56
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2104543; hg19: chr10-96429971;