10-81429197-C-T

Variant names:

• chr10-81429197-C-T
• rs1329201

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.28 in 152,024 control chromosomes in the GnomAD database, including 6,597 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 0.28 (6597 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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: 0.281 AC: 42613 AN: 151906 Hom.: 6594 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.280 AC: 42628 AN: 152024 Hom.: 6597 Cov.: 33 AF XY: 0.279 AC XY: 20717 AN XY: 74326

African (AFR) AF: 0.176 AC: 7292 AN: 41454

American (AMR) AF: 0.279 AC: 4262 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1372 AN: 3470

East Asian (EAS) AF: 0.0772 AC: 400 AN: 5180

South Asian (SAS) AF: 0.203 AC: 981 AN: 4824

European-Finnish (FIN) AF: 0.354 AC: 3731 AN: 10542

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23347 AN: 67968

Other (OTH) AF: 0.320 AC: 675 AN: 2108

Alfa AF: 0.272 Hom.: 4900

Bravo AF: 0.271

Asia WGS AF: 0.172 AC: 598 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.43
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1329201; hg19: chr10-83188953;