rs10935575

Positions:

• chr3-145606706-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 0.227 in 151,882 control chromosomes in the GnomAD database, including 4,247 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 (4247 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34470 AN: 151764 Hom.: 4243 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.227 AC: 34485 AN: 151882 Hom.: 4247 Cov.: 31 AF XY: 0.220 AC XY: 16345 AN XY: 74196

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.241

Alfa AF: 0.259 Hom.: 657

Bravo AF: 0.229

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.3
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10935575; hg19: chr3-145324493;