10-29957351-G-A

Position:

• chr10-29957351-G-A

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 0.107 in 152,068 control chromosomes in the GnomAD database, including 2,554 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 0.11 (2554 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16172 AN: 151950 Hom.: 2537 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0688

Gnomad FIN AF: 0.000850

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.00847

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.107 AC: 16227 AN: 152068 Hom.: 2554 Cov.: 33 AF XY: 0.104 AC XY: 7766 AN XY: 74322

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.0443

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.0680

Gnomad4 FIN AF: 0.000850

Gnomad4 NFE AF: 0.00848

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0168 Hom.: 39

Bravo AF: 0.120

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.98
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508755; hg19: chr10-30246280;