chr11-24225985-T-C

Variant names:

• chr11-24225985-T-C
• rs7131224

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 0.693 in 151,856 control chromosomes in the GnomAD database, including 36,770 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 0.69 (36770 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 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: 0.693 AC: 105199 AN: 151738 Hom.: 36723 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.693 AC: 105303 AN: 151856 Hom.: 36770 Cov.: 31 AF XY: 0.693 AC XY: 51459 AN XY: 74218

African (AFR) AF: 0.743 AC: 30778 AN: 41436

American (AMR) AF: 0.686 AC: 10453 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2459 AN: 3466

East Asian (EAS) AF: 0.481 AC: 2481 AN: 5160

South Asian (SAS) AF: 0.673 AC: 3239 AN: 4810

European-Finnish (FIN) AF: 0.660 AC: 6957 AN: 10538

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46507 AN: 67900

Other (OTH) AF: 0.710 AC: 1498 AN: 2110

Alfa AF: 0.685 Hom.: 70535

Bravo AF: 0.695

Asia WGS AF: 0.572 AC: 1986 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.40
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7131224; hg19: chr11-24247531;