rs2003206

Positions:

• chr7-67261232-A-C

Variant summary

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

The ENST00000685171.1(PMS2P4):​n.568+31231T>G 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 0.118 in 152,122 control chromosomes in the GnomAD database, including 1,328 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 0.12 (1328 hom., cov: 32)
• Consequence: PMS2P4 ENST00000685171.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821

Genes affected

PMS2P4 (HGNC:9129): (PMS1 homolog 2, mismatch repair system component pseudogene 4)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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
PMS2P4	ENST00000685171.1	n.568+31231T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17907 AN: 152004 Hom.: 1331 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0921

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0835

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.118 AC: 17911 AN: 152122 Hom.: 1328 Cov.: 32 AF XY: 0.115 AC XY: 8533 AN XY: 74370

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0835

Gnomad4 OTH AF: 0.103

Alfa AF: 0.106 Hom.: 161

Bravo AF: 0.124

Asia WGS AF: 0.0870 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.40
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2003206; hg19: chr7-66726219;