10-29346927-A-G

Variant names:

• chr10-29346927-A-G
• rs1751960

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 0.392 in 152,084 control chromosomes in the GnomAD database, including 12,061 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 0.39 (12061 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.912
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 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: 0.392 AC: 59562 AN: 151966 Hom.: 12043 Cov.: 33

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.392 AC: 59615 AN: 152084 Hom.: 12061 Cov.: 33 AF XY: 0.384 AC XY: 28536 AN XY: 74360

African (AFR) AF: 0.471 AC: 19528 AN: 41450

American (AMR) AF: 0.317 AC: 4846 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2563 AN: 5162

South Asian (SAS) AF: 0.266 AC: 1284 AN: 4824

European-Finnish (FIN) AF: 0.316 AC: 3344 AN: 10592

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25507 AN: 67982

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.381 Hom.: 48926

Bravo AF: 0.399

Asia WGS AF: 0.359 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.82
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs1751960; hg19: chr10-29635856;