6-29982433-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-5038T>C		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.223

Alfa AF: 0.264 Hom.: 3629

Bravo AF: 0.219

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs401618; hg19: chr6-29950210;