chr6-31182448-T-A

Position:

• chr6-31182448-T-A

Variant summary

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

The NR_152835.1(PSORS1C3):​n.292+3578A>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 0.0427 in 152,320 control chromosomes in the GnomAD database, including 220 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 0.043 (220 hom., cov: 31)
• Consequence: PSORS1C3 NR_152835.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

PSORS1C3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSORS1C3	NR_152835.1	n.292+3578A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0428 AC: 6510 AN: 152202 Hom.: 219 Cov.: 31

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0590

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0876

Gnomad FIN AF: 0.0392

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0457

Gnomad OTH AF: 0.0561

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

GnomAD4 genome AF: 0.0427 AC: 6507 AN: 152320 Hom.: 220 Cov.: 31 AF XY: 0.0440 AC XY: 3276 AN XY: 74484

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0588

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.0870

Gnomad4 FIN AF: 0.0392

Gnomad4 NFE AF: 0.0457

Gnomad4 OTH AF: 0.0570

Alfa AF: 0.0497 Hom.: 28

Bravo AF: 0.0429

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7760698; hg19: chr6-31150225;