10-29152418-C-T

Variant names:

• chr10-29152418-C-T
• rs564281

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 0.369 in 151,556 control chromosomes in the GnomAD database, including 11,195 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 0.37 (11195 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 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: 0.369 AC: 55911 AN: 151438 Hom.: 11205 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.369 AC: 55888 AN: 151556 Hom.: 11195 Cov.: 32 AF XY: 0.371 AC XY: 27492 AN XY: 74032

African (AFR) AF: 0.205 AC: 8468 AN: 41386

American (AMR) AF: 0.368 AC: 5610 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1501 AN: 3462

East Asian (EAS) AF: 0.257 AC: 1318 AN: 5136

South Asian (SAS) AF: 0.442 AC: 2123 AN: 4798

European-Finnish (FIN) AF: 0.488 AC: 5108 AN: 10468

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30337 AN: 67766

Other (OTH) AF: 0.410 AC: 862 AN: 2102

Alfa AF: 0.414 Hom.: 36432

Bravo AF: 0.351

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0040
DANN	Benign	0.90
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs564281; hg19: chr10-29441347;