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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;