rs11575254

Variant names:

• chr12-56340907-C-T
• rs11575254

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00517 in 119,342 control chromosomes in the GnomAD database, including 2 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 0.0052 (2 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS2: High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.00518 AC: 618 AN: 119272 Hom.: 2 Cov.: 28

Gnomad AFR AF: 0.00102

Gnomad AMI AF: 0.00114

Gnomad AMR AF: 0.00842

Gnomad ASJ AF: 0.0120

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00209

Gnomad FIN AF: 0.00386

Gnomad MID AF: 0.0299

Gnomad NFE AF: 0.00697

Gnomad OTH AF: 0.00434

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

GnomAD4 genome AF: 0.00517 AC: 617 AN: 119342 Hom.: 2 Cov.: 28 AF XY: 0.00499 AC XY: 274 AN XY: 54930

African (AFR) AF: 0.00102 AC: 31 AN: 30532

American (AMR) AF: 0.00841 AC: 72 AN: 8560

Ashkenazi Jewish (ASJ) AF: 0.0120 AC: 40 AN: 3344

East Asian (EAS) AF: 0.00 AC: 0 AN: 3410

South Asian (SAS) AF: 0.00210 AC: 7 AN: 3340

European-Finnish (FIN) AF: 0.00386 AC: 18 AN: 4668

Middle Eastern (MID) AF: 0.0317 AC: 4 AN: 126

European-Non Finnish (NFE) AF: 0.00695 AC: 437 AN: 62850

Other (OTH) AF: 0.00428 AC: 7 AN: 1634

Alfa AF: 0.0000533 Hom.: 0

Bravo AF: 0.00418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.62
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs11575254; hg19: chr12-56734691;