rs11171526

Variant names:

• chr12-55512677-T-A
• rs11171526
• ENST00000555138.2:n.143-19519A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555138.2(ENSG00000258763):​n.143-19519A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,984 control chromosomes in the GnomAD database, including 9,082 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 0.23 (9082 hom., cov: 31)
• Consequence: ENSG00000258763 ENST00000555138.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

Genes affected

ENSG00000258763 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555138.2. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000258763	ENST00000555138.2	TSL:2	n.143-19519A>T		intron	N/A
	ENSG00000258763	ENST00000556750.6	TSL:2	n.143-19519A>T		intron	N/A
	ENSG00000258763	ENST00000715996.1		n.643-19519A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34988 AN: 151866 Hom.: 9054 Cov.: 31

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0534

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0677

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.231 AC: 35072 AN: 151984 Hom.: 9082 Cov.: 31 AF XY: 0.224 AC XY: 16665 AN XY: 74322

African (AFR) AF: 0.645 AC: 26696 AN: 41384

American (AMR) AF: 0.123 AC: 1883 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3470

East Asian (EAS) AF: 0.101 AC: 520 AN: 5150

South Asian (SAS) AF: 0.0531 AC: 256 AN: 4824

European-Finnish (FIN) AF: 0.0444 AC: 471 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0677 AC: 4603 AN: 67948

Other (OTH) AF: 0.178 AC: 375 AN: 2112

Alfa AF: 0.155 Hom.: 710

Bravo AF: 0.254

Asia WGS AF: 0.137 AC: 476 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.87
DANN	Benign	0.41
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11171526;

hg19: chr12-55906461;