rs16896742

Variant names:

• chr6-29954963-A-G
• rs16896742
• ENST00000849678.1:n.589-8047T>C

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-8047T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,410 control chromosomes in the GnomAD database, including 7,052 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 0.35 (7052 hom., cov: 35)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 40 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849678.1. 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	ENST00000849678.1		n.589-8047T>C		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+21640T>C		intron	N/A
	POLR1HASP	ENST00000849682.1		n.750+21640T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53356 AN: 151292 Hom.: 7051 Cov.: 35

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.353 AC: 53387 AN: 151410 Hom.: 7052 Cov.: 35 AF XY: 0.353 AC XY: 26126 AN XY: 74026

African (AFR) AF: 0.322 AC: 13196 AN: 41040

American (AMR) AF: 0.372 AC: 5664 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 996 AN: 3458

East Asian (EAS) AF: 0.367 AC: 1893 AN: 5152

South Asian (SAS) AF: 0.317 AC: 1522 AN: 4798

European-Finnish (FIN) AF: 0.423 AC: 4472 AN: 10572

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24515 AN: 67880

Other (OTH) AF: 0.332 AC: 697 AN: 2100

Alfa AF: 0.378 Hom.: 12808

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.8
DANN	Benign	0.55
PhyloP100		0.14

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: rs16896742;

hg19: chr6-29922740;