rs1074145

Variant names:

• chr10-94922089-G-A
• rs1074145

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 0.166 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.174 AC: 7217 AN: 41404

American (AMR) AF: 0.129 AC: 1969 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3466

East Asian (EAS) AF: 0.296 AC: 1522 AN: 5144

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4810

European-Finnish (FIN) AF: 0.184 AC: 1932 AN: 10500

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9993 AN: 67926

Other (OTH) AF: 0.153 AC: 322 AN: 2104

Alfa AF: 0.152 Hom.: 536

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1074145; hg19: chr10-96681846;