rs2252070

chr11-102955810-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.668 in 1,529,566 control chromosomes in the GnomAD database, including 343,519 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.67 (34448 hom., cov: 32)
  • Exomes 𝑓: 0.67 (309071 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.38

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 11-102955810-C-T is Benign according to our data. Variant chr11-102955810-C-T is described in ClinVar as [Benign]. Clinvar id is 1166185.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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: 0.671 AC: 101897 AN: 151950 Hom.: 34424 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.660

GnomAD4 exome AF: 0.668 AC: 919882 AN: 1377498 Hom.: 309071 AF XY: 0.665 AC XY: 457185 AN XY: 687902

Gnomad4 AFR exome AF: 0.724

Gnomad4 AMR exome AF: 0.653

Gnomad4 ASJ exome AF: 0.583

Gnomad4 EAS exome AF: 0.469

Gnomad4 SAS exome AF: 0.602

Gnomad4 FIN exome AF: 0.628

Gnomad4 NFE exome AF: 0.684

Gnomad4 OTH exome AF: 0.652

GnomAD4 genome AF: 0.671 AC: 101978 AN: 152068 Hom.: 34448 Cov.: 32 AF XY: 0.662 AC XY: 49207 AN XY: 74318

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.657

Alfa AF: 0.681 Hom.: 3391

Bravo AF: 0.675

Asia WGS AF: 0.548 AC: 1907 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 16, 2018	This variant is associated with the following publications: (PMID: 27245877, 26635116, 12392760, 18308831) -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 22, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	12
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2252070; hg19: chr11-102826539; COSMIC: COSV52823914;