rs7758512

Variant names:

• chr6-30002812-T-G
• rs7758512
• ENST00000420251.5:n.709-80A>C

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.709-80A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,414 control chromosomes in the GnomAD database, including 2,744 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 0.17 (2742 hom., cov: 32)
  • Exomes 𝑓: 0.16 (2 hom.)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 47 publications found

Genes affected

POLR1HASP (HGNC:):

POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420251.5. 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
	POLR1HASP	NR_026751.2		n.714-80A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000420251.5	TSL:1	n.709-80A>C		intron	N/A
	POLR1HASP	ENST00000376797.7	TSL:2	n.1549-80A>C		intron	N/A
	POLR1HASP	ENST00000422224.6	TSL:3	n.823-14585A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25911 AN: 152032 Hom.: 2725 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.163 AC: 43 AN: 264 Hom.: 2 AF XY: 0.149 AC XY: 25 AN XY: 168

African (AFR) AF: 0.400 AC: 4 AN: 10

American (AMR) AF: 0.500 AC: 8 AN: 16

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.125 AC: 1 AN: 8

South Asian (SAS) AF: 0.0714 AC: 1 AN: 14

European-Finnish (FIN) AF: 0.133 AC: 4 AN: 30

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.148 AC: 24 AN: 162

Other (OTH) AF: 0.00 AC: 0 AN: 22

GnomAD4 genome AF: 0.171 AC: 25963 AN: 152150 Hom.: 2742 Cov.: 32 AF XY: 0.169 AC XY: 12554 AN XY: 74412

African (AFR) AF: 0.274 AC: 11388 AN: 41490

American (AMR) AF: 0.211 AC: 3219 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3464

East Asian (EAS) AF: 0.189 AC: 976 AN: 5168

South Asian (SAS) AF: 0.182 AC: 877 AN: 4820

European-Finnish (FIN) AF: 0.0475 AC: 504 AN: 10610

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7461 AN: 67996

Other (OTH) AF: 0.193 AC: 407 AN: 2110

Alfa AF: 0.145 Hom.: 4202

Bravo AF: 0.191

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-1.9

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: rs7758512;

hg19: chr6-29970589;