rs11970286

chr6-118359211-C-T

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 0.357 in 151,918 control chromosomes in the GnomAD database, including 10,558 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 0.36 (10558 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 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: 0.357 AC: 54164 AN: 151800 Hom.: 10561 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.357 AC: 54184 AN: 151918 Hom.: 10558 Cov.: 31 AF XY: 0.353 AC XY: 26184 AN XY: 74258

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.328

Alfa AF: 0.425 Hom.: 30737

Bravo AF: 0.335

Asia WGS AF: 0.296 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.43
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11970286; hg19: chr6-118680374;