6-29974166-C-T

Variant names:

• chr6-29974166-C-T
• rs2523946

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 0.483 in 150,646 control chromosomes in the GnomAD database, including 17,708 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 0.48 (17708 hom., cov: 28)
• Consequence: MICD intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 74 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICD		n.29974166C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000849678.1	n.589-27250G>A		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+2437G>A		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1	n.506-17416G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.482 AC: 72629 AN: 150532 Hom.: 17682 Cov.: 28

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.483 AC: 72700 AN: 150646 Hom.: 17708 Cov.: 28 AF XY: 0.480 AC XY: 35332 AN XY: 73546

African (AFR) AF: 0.539 AC: 22014 AN: 40830

American (AMR) AF: 0.528 AC: 7998 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1314 AN: 3460

East Asian (EAS) AF: 0.450 AC: 2297 AN: 5102

South Asian (SAS) AF: 0.406 AC: 1934 AN: 4764

European-Finnish (FIN) AF: 0.481 AC: 5012 AN: 10412

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30633 AN: 67660

Other (OTH) AF: 0.479 AC: 997 AN: 2082

Alfa AF: 0.458 Hom.: 65006

Bravo AF: 0.497

Asia WGS AF: 0.416 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.52
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2523946; hg19: chr6-29941943;