chr6-29938914-A-G

Variant names:

• chr6-29938914-A-G
• rs2860580
• ENST00000849679.1:n.66-10368T>C

Variant summary

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

The ENST00000849679.1(POLR1HASP):​n.66-10368T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 150,544 control chromosomes in the GnomAD database, including 25,653 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 0.58 (25653 hom., cov: 31)
• Consequence: POLR1HASP ENST00000849679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 81 publications found

Genes affected

POLR1HASP (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901298	XR_007059541.1	n.813+5867T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000849679.1	n.66-10368T>C		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849682.1	n.751-10368T>C		intron_variant	Intron 1 of 3
POLR1HASP	ENST00000849693.1	n.1099+5867T>C		intron_variant	Intron 1 of 1
POLR1HASP	ENST00000849697.1	n.280-10368T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.585 AC: 87962 AN: 150430 Hom.: 25613 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.585 AC: 88056 AN: 150544 Hom.: 25653 Cov.: 31 AF XY: 0.585 AC XY: 43062 AN XY: 73642

African (AFR) AF: 0.584 AC: 23617 AN: 40442

American (AMR) AF: 0.652 AC: 9851 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2204 AN: 3440

East Asian (EAS) AF: 0.673 AC: 3467 AN: 5150

South Asian (SAS) AF: 0.567 AC: 2722 AN: 4798

European-Finnish (FIN) AF: 0.554 AC: 5848 AN: 10552

Middle Eastern (MID) AF: 0.595 AC: 169 AN: 284

European-Non Finnish (NFE) AF: 0.567 AC: 38409 AN: 67750

Other (OTH) AF: 0.594 AC: 1244 AN: 2096

Alfa AF: 0.573 Hom.: 63430

Bravo AF: 0.589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.26
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2860580; hg19: chr6-29906691;