6-29982433-A-G

Variant names:

• chr6-29982433-A-G
• rs401618
• ENST00000688495.1:n.361-5038T>C

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-5038T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,518 control chromosomes in the GnomAD database, including 4,554 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 0.23 (4554 hom., cov: 32)
• Consequence: POLR1HASP ENST00000688495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 24 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 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

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	ENST00000688495.1		n.361-5038T>C		intron	N/A
	POLR1HASP	ENST00000849678.1		n.589-35517T>C		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-25683T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35370 AN: 151408 Hom.: 4544 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.234 AC: 35389 AN: 151518 Hom.: 4554 Cov.: 32 AF XY: 0.237 AC XY: 17546 AN XY: 74000

African (AFR) AF: 0.118 AC: 4879 AN: 41210

American (AMR) AF: 0.229 AC: 3485 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1503 AN: 5160

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4814

European-Finnish (FIN) AF: 0.328 AC: 3430 AN: 10472

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18938 AN: 67872

Other (OTH) AF: 0.223 AC: 469 AN: 2100

Alfa AF: 0.263 Hom.: 15054

Bravo AF: 0.219

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.48
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs401618; hg19: chr6-29950210;