rs2104543

Positions:

• chr10-94670214-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;