rs11575088

Variant names:

• chr6-167143546-C-A
• rs11575088

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 0.139 in 152,278 control chromosomes in the GnomAD database, including 1,832 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 0.14 (1832 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 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: 0.139 AC: 21201 AN: 152160 Hom.: 1832 Cov.: 33

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.139 AC: 21211 AN: 152278 Hom.: 1832 Cov.: 33 AF XY: 0.134 AC XY: 9997 AN XY: 74466

African (AFR) AF: 0.0573 AC: 2383 AN: 41568

American (AMR) AF: 0.138 AC: 2112 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 764 AN: 3462

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.130 AC: 626 AN: 4820

European-Finnish (FIN) AF: 0.111 AC: 1183 AN: 10618

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13487 AN: 67998

Other (OTH) AF: 0.162 AC: 343 AN: 2114

Alfa AF: 0.156 Hom.: 1281

Bravo AF: 0.139

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs11575088; hg19: chr6-167557034; COSMIC: COSV59476054;