10-83868459-C-T

Variant names:

• chr10-83868459-C-T
• rs11200713

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 0.403 in 151,642 control chromosomes in the GnomAD database, including 12,403 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 0.40 (12403 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 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: 0.403 AC: 61014 AN: 151522 Hom.: 12379 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.403 AC: 61088 AN: 151642 Hom.: 12403 Cov.: 31 AF XY: 0.400 AC XY: 29636 AN XY: 74112

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.440

Alfa AF: 0.424 Hom.: 27228

Bravo AF: 0.416

Asia WGS AF: 0.323 AC: 1122 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	0.89
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11200713; hg19: chr10-85628215;