rs9260997

Variant names:

• chr6-29995539-T-C
• rs9260997
• ENST00000422224.6:n.823-7312A>G

Variant summary

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

The ENST00000422224.6(POLR1HASP):​n.823-7312A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,320 control chromosomes in the GnomAD database, including 61,635 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 0.90 (61635 hom., cov: 35)
• Consequence: POLR1HASP ENST00000422224.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 11 publications found

Genes affected

POLR1HASP (HGNC:):

MCCD1P2 (HGNC:33462): (mitochondrial coiled-coil domain 1 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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
POLR1HASP	ENST00000422224.6	n.823-7312A>G		intron_variant	Intron 5 of 5	3
POLR1HASP	ENST00000688495.1	n.361-18144A>G		intron_variant	Intron 3 of 3
POLR1HASP	ENST00000849678.1	n.588+26128A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136776 AN: 152202 Hom.: 61572 Cov.: 35

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.899 AC: 136898 AN: 152320 Hom.: 61635 Cov.: 35 AF XY: 0.900 AC XY: 67020 AN XY: 74490

African (AFR) AF: 0.920 AC: 38217 AN: 41562

American (AMR) AF: 0.917 AC: 14032 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3152 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5120 AN: 5188

South Asian (SAS) AF: 0.945 AC: 4563 AN: 4828

European-Finnish (FIN) AF: 0.891 AC: 9468 AN: 10628

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.872 AC: 59325 AN: 68016

Other (OTH) AF: 0.895 AC: 1893 AN: 2116

Alfa AF: 0.887 Hom.: 118380

Bravo AF: 0.903

Asia WGS AF: 0.960 AC: 3340 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	3.5
DANN	Benign	0.66
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs9260997; hg19: chr6-29963316;