rs1074145

Positions:

• chr10-94922089-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 0.166 in 151,796 control chromosomes in the GnomAD database, including 2,255 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 0.17 (2255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

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 (SAS) allele frequency at 95% confidence interval = 0.304 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: 0.166 AC: 25110 AN: 151678 Hom.: 2251 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.166 AC: 25127 AN: 151796 Hom.: 2255 Cov.: 32 AF XY: 0.169 AC XY: 12561 AN XY: 74172

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.153

Alfa AF: 0.145 Hom.: 315

Bravo AF: 0.159

Asia WGS AF: 0.290 AC: 1005 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.76
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074145; hg19: chr10-96681846;