chr6-31125810-G-A

Variant names:

• chr6-31125810-G-A
• rs3815087
• NM_014068.3:c.-94G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014068.3(PSORS1C1):​c.-94G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,184 control chromosomes in the GnomAD database, including 5,120 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 0.25 (5117 hom., cov: 33)
  • Exomes 𝑓: 0.36 (3 hom.)
• Consequence: PSORS1C1 NM_014068.3 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 58 publications found

Genes affected

PSORS1C1 (HGNC:17202): (psoriasis susceptibility 1 candidate 1) This gene is one of several genes thought to confer susceptibility to psoriasis and systemic sclerosis, located on chromosome 6 near the major histocompatibility complex (MHC) class I region. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014068.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	NM_014068.3	MANE Select	c.-94G>A		5_prime_UTR_premature_start_codon_gain	Exon 2 of 6	NP_054787.2	Q9UIG5-1
	PSORS1C1	NM_014068.3	MANE Select	c.-94G>A		5_prime_UTR	Exon 2 of 6	NP_054787.2	Q9UIG5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSORS1C1	ENST00000259881.10	TSL:1 MANE Select	c.-94G>A		5_prime_UTR_premature_start_codon_gain	Exon 2 of 6	ENSP00000259881.9	Q9UIG5-1
	PSORS1C1	ENST00000259881.10	TSL:1 MANE Select	c.-94G>A		5_prime_UTR	Exon 2 of 6	ENSP00000259881.9	Q9UIG5-1
	PSORS1C1	ENST00000479581.5	TSL:1	n.61+10919G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37805 AN: 152030 Hom.: 5113 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.277

GnomAD4 exome AF: 0.361 AC: 13 AN: 36 Hom.: 3 Cov.: 0 AF XY: 0.367 AC XY: 11 AN XY: 30

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 2 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.350 AC: 7 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.249 AC: 37830 AN: 152148 Hom.: 5117 Cov.: 33 AF XY: 0.252 AC XY: 18768 AN XY: 74398

African (AFR) AF: 0.326 AC: 13531 AN: 41494

American (AMR) AF: 0.215 AC: 3296 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1439 AN: 3468

East Asian (EAS) AF: 0.269 AC: 1392 AN: 5170

South Asian (SAS) AF: 0.338 AC: 1630 AN: 4820

European-Finnish (FIN) AF: 0.206 AC: 2183 AN: 10594

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13457 AN: 68000

Other (OTH) AF: 0.275 AC: 579 AN: 2104

Alfa AF: 0.220 Hom.: 16463

Bravo AF: 0.253

Asia WGS AF: 0.286 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.60
PhyloP100		-1.1
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3815087; hg19: chr6-31093587;