rs16896944

Variant names:

• chr6-30058369-T-C
• rs16896944
• ENST00000452229.3:n.396A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-30058369-T-C
• chr6-30058369-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000452229.3(POLR1HASP):​n.396A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,674 control chromosomes in the GnomAD database, including 772 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 0.070 (772 hom., cov: 32)
  • Exomes 𝑓: 0.011 (0 hom.)
• Consequence: POLR1HASP ENST00000452229.3 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.42
• Publications: 12 publications found

Genes affected

POLR1HASP (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452229.3. 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_145417.1		n.364A>G		splice_region non_coding_transcript_exon	Exon 1 of 3
	POLR1HASP	NR_026751.2		n.367-179A>G		intron	N/A
	POLR1HASP	NR_145416.1		n.367-179A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000452229.3	TSL:1	n.396A>G		splice_region non_coding_transcript_exon	Exon 1 of 3
	POLR1HASP	ENST00000420251.5	TSL:1	n.362-179A>G		intron	N/A
	POLR1HASP	ENST00000431012.5	TSL:1	n.102-179A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 10705 AN: 152120 Hom.: 772 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0436

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0291

Gnomad OTH AF: 0.0813

GnomAD4 exome AF: 0.0115 AC: 5 AN: 436 Hom.: 0 Cov.: 0 AF XY: 0.0152 AC XY: 4 AN XY: 264

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00935 AC: 4 AN: 428

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.0704 AC: 10711 AN: 152238 Hom.: 772 Cov.: 32 AF XY: 0.0671 AC XY: 4998 AN XY: 74442

African (AFR) AF: 0.179 AC: 7447 AN: 41492

American (AMR) AF: 0.0553 AC: 846 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0436 AC: 151 AN: 3466

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.0118 AC: 57 AN: 4830

European-Finnish (FIN) AF: 0.00264 AC: 28 AN: 10626

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0291 AC: 1978 AN: 68018

Other (OTH) AF: 0.0800 AC: 169 AN: 2112

Alfa AF: 0.0431 Hom.: 1132

Bravo AF: 0.0807

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	15
DANN	Benign	0.76
PhyloP100		3.4
Mutation Taster		=75/25	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs16896944; hg19: chr6-30026146;