6-29950325-T-G

Variant names:

• chr6-29950325-T-G
• rs9260378
• ENST00000849678.1:n.589-3409A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000849678.1(POLR1HASP):​n.589-3409A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0035 (0 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 2 publications found

Genes affected

POLR1HASP (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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.589-3409A>C		intron	N/A
	POLR1HASP	ENST00000849679.1		n.66-21779A>C		intron	N/A
	POLR1HASP	ENST00000849682.1		n.751-21779A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00352 AC: 497 AN: 141134 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00835

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00503

Gnomad ASJ AF: 0.00156

Gnomad EAS AF: 0.00604

Gnomad SAS AF: 0.00820

Gnomad FIN AF: 0.000287

Gnomad MID AF: 0.00352

Gnomad NFE AF: 0.000734

Gnomad OTH AF: 0.00261

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00354 AC: 500 AN: 141228 Hom.: 0 Cov.: 32 AF XY: 0.00334 AC XY: 231 AN XY: 69240

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00832 AC: 301 AN: 36178

American (AMR) AF: 0.00517 AC: 72 AN: 13936

Ashkenazi Jewish (ASJ) AF: 0.00156 AC: 5 AN: 3196

East Asian (EAS) AF: 0.00606 AC: 28 AN: 4620

South Asian (SAS) AF: 0.00844 AC: 37 AN: 4386

European-Finnish (FIN) AF: 0.000287 AC: 3 AN: 10454

Middle Eastern (MID) AF: 0.00379 AC: 1 AN: 264

European-Non Finnish (NFE) AF: 0.000734 AC: 48 AN: 65360

Other (OTH) AF: 0.00260 AC: 5 AN: 1926

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00110 Hom.: 9

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.26
PhyloP100		-1.9

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: rs9260378;

hg19: chr6-29918102;