rs558275

Positions:

• chr12-120759088-A-G

Variant summary

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

The ENST00000542620.1(ENSG00000255946):​n.202+2303T>C 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 0.71 in 152,004 control chromosomes in the GnomAD database, including 39,696 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 0.71 (39696 hom., cov: 30)
• Consequence: ENST00000542620.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000542620.1	n.202+2303T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000685547.2	n.2536T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107867 AN: 151884 Hom.: 39641 Cov.: 30

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.710 AC: 107981 AN: 152004 Hom.: 39696 Cov.: 30 AF XY: 0.717 AC XY: 53261 AN XY: 74304

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.685

Alfa AF: 0.638 Hom.: 14338

Bravo AF: 0.731

Asia WGS AF: 0.811 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs558275; hg19: chr12-121196891;