rs11961455

Variant names:

• chr6-89085569-G-C
• rs11961455

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.397 in 152,088 control chromosomes in the GnomAD database, including 12,633 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 0.40 (12633 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60414 AN: 151972 Hom.: 12627 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.397 AC: 60437 AN: 152088 Hom.: 12633 Cov.: 33 AF XY: 0.408 AC XY: 30298 AN XY: 74350

African (AFR) AF: 0.294 AC: 12208 AN: 41500

American (AMR) AF: 0.452 AC: 6900 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1344 AN: 3472

East Asian (EAS) AF: 0.684 AC: 3540 AN: 5178

South Asian (SAS) AF: 0.467 AC: 2257 AN: 4828

European-Finnish (FIN) AF: 0.495 AC: 5214 AN: 10540

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27777 AN: 67986

Other (OTH) AF: 0.368 AC: 778 AN: 2112

Alfa AF: 0.406 Hom.: 1591

Bravo AF: 0.390

Asia WGS AF: 0.502 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs11961455; hg19: chr6-89795288;