rs12542166

Positions:

• chr8-121970599-A-C

Variant summary

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

The variant allele was found at a frequency of 0.0675 in 152,242 control chromosomes in the GnomAD database, including 438 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 0.067 (438 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.704

Genes affected

ENSG00000254303 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.121970599A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254303	ENST00000523792.1	n.281+11018T>G		intron_variant		1
HAS2-AS1	ENST00000647560.1	n.447-22999A>C		intron_variant
HAS2-AS1	ENST00000653591.1	n.764-22999A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10254 AN: 152124 Hom.: 435 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.0622

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

GnomAD4 genome AF: 0.0675 AC: 10274 AN: 152242 Hom.: 438 Cov.: 32 AF XY: 0.0685 AC XY: 5097 AN XY: 74434

Gnomad4 AFR AF: 0.0168

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.0589

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0862

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0785 Hom.: 140

Bravo AF: 0.0619

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12542166; hg19: chr8-122982838;