6-29972108-G-A

Variant names:

• chr6-29972108-G-A
• rs380924

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 0.559 in 391,354 control chromosomes in the GnomAD database, including 62,514 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 0.53 (22357 hom., cov: 30)
  • Exomes 𝑓: 0.57 (40157 hom.)
• Consequence: MICD intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413248.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICD	ENST00000413248.1	TSL:6	n.256+101C>T		intron	N/A
	POLR1HASP	ENST00000849678.1		n.589-25192C>T		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+4495C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81104 AN: 151548 Hom.: 22353 Cov.: 30

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.501

GnomAD4 exome AF: 0.574 AC: 137502 AN: 239688 Hom.: 40157 Cov.: 0 AF XY: 0.569 AC XY: 70764 AN XY: 124340

African (AFR) AF: 0.422 AC: 3129 AN: 7406

American (AMR) AF: 0.533 AC: 6172 AN: 11574

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 3567 AN: 7876

East Asian (EAS) AF: 0.602 AC: 10701 AN: 17788

South Asian (SAS) AF: 0.461 AC: 8037 AN: 17450

European-Finnish (FIN) AF: 0.668 AC: 10063 AN: 15056

Middle Eastern (MID) AF: 0.508 AC: 594 AN: 1170

European-Non Finnish (NFE) AF: 0.594 AC: 86961 AN: 146474

Other (OTH) AF: 0.556 AC: 8278 AN: 14894

GnomAD4 genome AF: 0.535 AC: 81121 AN: 151666 Hom.: 22357 Cov.: 30 AF XY: 0.536 AC XY: 39702 AN XY: 74104

African (AFR) AF: 0.420 AC: 17356 AN: 41292

American (AMR) AF: 0.507 AC: 7732 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1550 AN: 3464

East Asian (EAS) AF: 0.560 AC: 2874 AN: 5130

South Asian (SAS) AF: 0.464 AC: 2229 AN: 4802

European-Finnish (FIN) AF: 0.691 AC: 7260 AN: 10506

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40255 AN: 67900

Other (OTH) AF: 0.506 AC: 1066 AN: 2108

Alfa AF: 0.438 Hom.: 1339

Bravo AF: 0.518

Asia WGS AF: 0.554 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.084
DANN	Benign	0.51
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs380924; hg19: chr6-29939885; COSMIC: COSV65136215;