chr12-63690554-A-G

Variant names:

• chr12-63690554-A-G
• rs11175121

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 0.0442 in 152,226 control chromosomes in the GnomAD database, including 294 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 0.044 (294 hom., cov: 33)
• Consequence: LOC100418730 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 1 publications found

Genes affected

LOC100418730 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509615.2. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000249753	ENST00000509615.2	TSL:5	n.239-66730T>C		intron	N/A
	ENSG00000290896	ENST00000541353.3	TSL:5	n.153-2062T>C		intron	N/A
	ENSG00000255583	ENST00000543539.1	TSL:6	n.234-2061T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0443 AC: 6733 AN: 152108 Hom.: 297 Cov.: 33

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0210

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.00980

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0442 AC: 6728 AN: 152226 Hom.: 294 Cov.: 33 AF XY: 0.0449 AC XY: 3341 AN XY: 74434

African (AFR) AF: 0.0909 AC: 3777 AN: 41530

American (AMR) AF: 0.0210 AC: 321 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3472

East Asian (EAS) AF: 0.118 AC: 609 AN: 5178

South Asian (SAS) AF: 0.133 AC: 640 AN: 4816

European-Finnish (FIN) AF: 0.00980 AC: 104 AN: 10612

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0165 AC: 1122 AN: 68002

Other (OTH) AF: 0.0426 AC: 90 AN: 2112

Alfa AF: 0.0282 Hom.: 23

Bravo AF: 0.0446

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.72
DANN	Benign	0.32
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs11175121; hg19: chr12-64084334;