rs11102522

Positions:

• chr1-112708266-T-C

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 0.191 in 152,230 control chromosomes in the GnomAD database, including 3,548 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 0.19 (3548 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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: 0.191 AC: 29007 AN: 152112 Hom.: 3548 Cov.: 33

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.191 AC: 29008 AN: 152230 Hom.: 3548 Cov.: 33 AF XY: 0.200 AC XY: 14922 AN XY: 74432

Gnomad4 AFR AF: 0.0839

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.182

Alfa AF: 0.197 Hom.: 3026

Bravo AF: 0.187

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11102522; hg19: chr1-113250888; COSMIC: COSV53517010; COSMIC: COSV53517010;