rs380924

Variant names:

• chr6-29972108-G-A
• rs380924

Your query was ambiguous. Multiple possible variants found:

• chr6-29972108-G-A
• chr6-29972108-G-C
• chr6-29972108-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICD		n.29972108G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICD	ENST00000413248.1	n.256+101C>T		intron_variant	Intron 1 of 2	6
POLR1HASP	ENST00000849678.1	n.589-25192C>T		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+4495C>T		intron_variant	Intron 1 of 5

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 v4.3

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;