chr6-31181268-C-T

Position:

• chr6-31181268-C-T

Variant summary

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

The NR_152835.1(PSORS1C3):​n.292+4758G>A 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 0.0885 in 137,996 control chromosomes in the GnomAD database, including 742 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 0.088 (742 hom., cov: 28)
• Consequence: PSORS1C3 NR_152835.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

PSORS1C3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSORS1C3	NR_152835.1	n.292+4758G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0883 AC: 12172 AN: 137888 Hom.: 737 Cov.: 28

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0157

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0747

Gnomad EAS AF: 0.0842

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0885 AC: 12207 AN: 137996 Hom.: 742 Cov.: 28 AF XY: 0.0876 AC XY: 5871 AN XY: 67008

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0867

Gnomad4 ASJ AF: 0.0747

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.0577

Gnomad4 FIN AF: 0.0104

Gnomad4 NFE AF: 0.0530

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0581 Hom.: 150

Bravo AF: 0.0906

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9263827; hg19: chr6-31149045;