chr6-29852501-A-G

Variant names:

• chr6-29852501-A-G
• rs3115627

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 0.308 in 152,216 control chromosomes in the GnomAD database, including 7,307 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 0.31 (7296 hom., cov: 32)
  • Exomes 𝑓: 0.33 (11 hom.)
• Consequence: MICF intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 21 publications found

Genes affected

MICF (HGNC:16801): (MHC class I polypeptide-related sequence F (pseudogene))

ENSG00000290870 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647952.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290870	ENST00000647952.1		n.2156-15T>C		intron	N/A
	ENSG00000285799	ENST00000432679.1	TSL:6	n.-10T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46763 AN: 151842 Hom.: 7283 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.332 AC: 85 AN: 256 Hom.: 11 Cov.: 0 AF XY: 0.307 AC XY: 43 AN XY: 140

African (AFR) AF: 0.500 AC: 3 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.300 AC: 3 AN: 10

European-Finnish (FIN) AF: 0.315 AC: 34 AN: 108

Middle Eastern (MID) AF: 0.321 AC: 18 AN: 56

European-Non Finnish (NFE) AF: 0.333 AC: 18 AN: 54

Other (OTH) AF: 0.400 AC: 8 AN: 20

GnomAD4 genome AF: 0.308 AC: 46792 AN: 151960 Hom.: 7296 Cov.: 32 AF XY: 0.305 AC XY: 22648 AN XY: 74274

African (AFR) AF: 0.281 AC: 11636 AN: 41396

American (AMR) AF: 0.294 AC: 4498 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3468

East Asian (EAS) AF: 0.363 AC: 1878 AN: 5172

South Asian (SAS) AF: 0.166 AC: 798 AN: 4814

European-Finnish (FIN) AF: 0.345 AC: 3651 AN: 10588

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22547 AN: 67926

Other (OTH) AF: 0.293 AC: 620 AN: 2114

Alfa AF: 0.322 Hom.: 18974

Bravo AF: 0.308

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.35
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs3115627; hg19: chr6-29820278;