11-67583461-G-T

Position:

• chr11-67583461-G-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 0.375 in 203,320 control chromosomes in the GnomAD database, including 15,119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.37 (11016 hom., cov: 32)
  • Exomes 𝑓: 0.38 (4103 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.249

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 11-67583461-G-T is Benign according to our data. Variant chr11-67583461-G-T is described in ClinVar as [Benign]. Clinvar id is 1237952.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 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: 0.373 AC: 56574 AN: 151606 Hom.: 11015 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.381 AC: 19675 AN: 51610 Hom.: 4103 AF XY: 0.382 AC XY: 9982 AN XY: 26120

Gnomad4 AFR exome AF: 0.381

Gnomad4 AMR exome AF: 0.256

Gnomad4 ASJ exome AF: 0.275

Gnomad4 EAS exome AF: 0.150

Gnomad4 SAS exome AF: 0.311

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.428

Gnomad4 OTH exome AF: 0.372

GnomAD4 genome AF: 0.373 AC: 56592 AN: 151710 Hom.: 11016 Cov.: 32 AF XY: 0.362 AC XY: 26840 AN XY: 74112

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.366

Alfa AF: 0.245 Hom.: 554

Bravo AF: 0.370

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17593068; hg19: chr11-67350932; COSMIC: COSV66992393;