rs3807031

Variant names:

• chr6-30066107-C-A
• rs3807031
• XM_047419279.1:c.-552-752C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-30066107-C-A
• chr6-30066107-C-G

Variant summary

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

The ENST00000849686.1(POLR1HASP):​n.170+773G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,018 control chromosomes in the GnomAD database, including 2,722 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 0.18 (2722 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896
• Publications: 34 publications found

Genes affected

PPP1R11 (HGNC:9285): (protein phosphatase 1 regulatory inhibitor subunit 11) This gene encodes a specific inhibitor of protein phosphatase-1 (PP1) with a differential sensitivity toward the metal-independent and metal-dependent forms of PP1. The gene is located within the major histocompatibility complex class I region on chromosome 6. [provided by RefSeq, Jul 2008]

POLR1HASP (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849686.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000849686.1		n.170+773G>T		intron	N/A
	POLR1HASP	ENST00000849687.1		n.132+773G>T		intron	N/A
	POLR1HASP	ENST00000849695.1		n.172+773G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27248 AN: 151900 Hom.: 2722 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.179 AC: 27247 AN: 152018 Hom.: 2722 Cov.: 32 AF XY: 0.181 AC XY: 13416 AN XY: 74262

African (AFR) AF: 0.115 AC: 4750 AN: 41460

American (AMR) AF: 0.172 AC: 2626 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1279 AN: 5172

South Asian (SAS) AF: 0.121 AC: 583 AN: 4812

European-Finnish (FIN) AF: 0.289 AC: 3042 AN: 10534

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 13998 AN: 67974

Other (OTH) AF: 0.138 AC: 292 AN: 2110

Alfa AF: 0.192 Hom.: 13081

Bravo AF: 0.169

Asia WGS AF: 0.148 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.4
DANN	Benign	0.74
PhyloP100		-0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3807031;

hg19: chr6-30033884;