rs11171526

chr12-55512677-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556750.5(ENSG00000258763):n.58-19519A>T variant causes a intron, non coding transcript 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: ENST00000556750.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000556750.5	n.58-19519A>T		intron_variant, non_coding_transcript_variant		2
	ENST00000555138.1	n.58-19519A>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0556

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0531

Gnomad4 FIN AF: 0.0444

Gnomad4 NFE AF: 0.0677

Gnomad4 OTH AF: 0.178

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.87
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11171526; hg19: chr12-55906461;