rs11995252

Variant names:

• chr8-121609669-T-C
• rs11995252

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 0.105 in 152,208 control chromosomes in the GnomAD database, including 1,268 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 0.11 (1268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15988 AN: 152090 Hom.: 1265 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.105 AC: 16010 AN: 152208 Hom.: 1268 Cov.: 32 AF XY: 0.104 AC XY: 7732 AN XY: 74420

African (AFR) AF: 0.219 AC: 9077 AN: 41488

American (AMR) AF: 0.0549 AC: 840 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 285 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5178

South Asian (SAS) AF: 0.103 AC: 496 AN: 4822

European-Finnish (FIN) AF: 0.0487 AC: 517 AN: 10622

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0665 AC: 4526 AN: 68014

Other (OTH) AF: 0.0852 AC: 180 AN: 2112

Alfa AF: 0.0778 Hom.: 1116

Bravo AF: 0.109

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.69
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs11995252; hg19: chr8-122621909;