10-29148963-C-T

Variant names:

• chr10-29148963-C-T
• rs533844

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 0.701 in 152,136 control chromosomes in the GnomAD database, including 37,641 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 0.70 (37641 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.768 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: 0.701 AC: 106633 AN: 152018 Hom.: 37634 Cov.: 34

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.701 AC: 106665 AN: 152136 Hom.: 37641 Cov.: 34 AF XY: 0.698 AC XY: 51879 AN XY: 74364

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.704

Alfa AF: 0.731 Hom.: 51012

Bravo AF: 0.695

Asia WGS AF: 0.669 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs533844; hg19: chr10-29437892;