chr6-29987248-T-C

Variant names:

• chr6-29987248-T-C
• rs3901554
• ENST00000688495.1:n.361-9853A>G

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-9853A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 152,208 control chromosomes in the GnomAD database, including 259 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 0.053 (259 hom., cov: 33)
• Consequence: POLR1HASP ENST00000688495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688495.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000688495.1		n.361-9853A>G		intron	N/A
	POLR1HASP	ENST00000849678.1		n.588+34419A>G		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-30498A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0527 AC: 8009 AN: 152090 Hom.: 259 Cov.: 33

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0388

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0516

Gnomad OTH AF: 0.0587

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

GnomAD4 genome AF: 0.0527 AC: 8023 AN: 152208 Hom.: 259 Cov.: 33 AF XY: 0.0531 AC XY: 3955 AN XY: 74434

African (AFR) AF: 0.0493 AC: 2046 AN: 41504

American (AMR) AF: 0.0632 AC: 966 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3466

East Asian (EAS) AF: 0.0389 AC: 202 AN: 5188

South Asian (SAS) AF: 0.0605 AC: 292 AN: 4830

European-Finnish (FIN) AF: 0.0238 AC: 252 AN: 10610

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0516 AC: 3506 AN: 68002

Other (OTH) AF: 0.0577 AC: 122 AN: 2116

Alfa AF: 0.0536 Hom.: 342

Bravo AF: 0.0538

Asia WGS AF: 0.0450 AC: 156 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	7.6
DANN	Benign	0.65
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs3901554; hg19: chr6-29955025;