6-29974306-C-T

Variant names:

• chr6-29974306-C-T
• rs3823355

Variant summary

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

The variant allele was found at a frequency of 0.263 in 151,142 control chromosomes in the GnomAD database, including 5,497 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 0.26 (5497 hom., cov: 28)
• Consequence: MICD intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 41 publications found

Genes affected

MICD (HGNC:7093): (MHC class I polypeptide-related sequence D (pseudogene))

POLR1HASP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

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.589-27390G>A		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+2297G>A		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-17556G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39701 AN: 151024 Hom.: 5497 Cov.: 28

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.263 AC: 39697 AN: 151142 Hom.: 5497 Cov.: 28 AF XY: 0.263 AC XY: 19355 AN XY: 73722

African (AFR) AF: 0.200 AC: 8231 AN: 41124

American (AMR) AF: 0.252 AC: 3823 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1593 AN: 5116

South Asian (SAS) AF: 0.170 AC: 808 AN: 4756

European-Finnish (FIN) AF: 0.364 AC: 3782 AN: 10382

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 19982 AN: 67796

Other (OTH) AF: 0.236 AC: 497 AN: 2104

Alfa AF: 0.277 Hom.: 23827

Bravo AF: 0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.63
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs3823355; hg19: chr6-29942083;