rs2003206

Variant names:

• chr7-67261232-A-C
• rs2003206
• ENST00000684859.1:n.517+34386T>G

Variant summary

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

The ENST00000684859.1(PMS2P4):​n.517+34386T>G variant causes a intron 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 ENST00000684859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821

Genes affected

PMS2P4 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PMS2P4	ENST00000684859.1	n.517+34386T>G		intron_variant	Intron 4 of 4
PMS2P4	ENST00000685171.1	n.568+31231T>G		intron_variant	Intron 5 of 5
PMS2P4	ENST00000685318.1	n.601+31231T>G		intron_variant	Intron 5 of 5

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;