chr12-121123168-T-C

Variant names:

• chr12-121123168-T-C
• rs11065441

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 0.108 in 152,128 control chromosomes in the GnomAD database, including 1,508 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 (1508 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 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: 0.108 AC: 16379 AN: 152010 Hom.: 1504 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.108 AC: 16404 AN: 152128 Hom.: 1508 Cov.: 31 AF XY: 0.109 AC XY: 8123 AN XY: 74366

African (AFR) AF: 0.233 AC: 9648 AN: 41454

American (AMR) AF: 0.0460 AC: 703 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1352 AN: 5164

South Asian (SAS) AF: 0.126 AC: 606 AN: 4816

European-Finnish (FIN) AF: 0.0792 AC: 840 AN: 10606

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0433 AC: 2944 AN: 68008

Other (OTH) AF: 0.0771 AC: 163 AN: 2114

Alfa AF: 0.0645 Hom.: 874

Bravo AF: 0.110

Asia WGS AF: 0.200 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.88
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs11065441; hg19: chr12-121560971;