chr10-116055375-G-A

Position:

• chr10-116055375-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 0.232 in 152,086 control chromosomes in the GnomAD database, including 4,903 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 0.23 (4903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.232 AC: 35298 AN: 151968 Hom.: 4894 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.232 AC: 35342 AN: 152086 Hom.: 4903 Cov.: 32 AF XY: 0.230 AC XY: 17118 AN XY: 74348

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.228

Alfa AF: 0.151 Hom.: 385

Bravo AF: 0.235

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.18
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: rs180557; hg19: chr10-117814886;