rs2734982

Variant names:

• chr6-29853790-G-T
• rs2734982

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 0.258 in 152,128 control chromosomes in the GnomAD database, including 5,301 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 (5301 hom., cov: 34)
• Consequence: MICF intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 14 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICF		n.29853790G>T		intragenic_variant
LOC105375010	XR_926680.3	n.42-1304C>A		intron_variant	Intron 1 of 2
LOC105375010	XR_926681.2	n.42-1304C>A		intron_variant	Intron 1 of 3
LOC105375010	XR_926682.3	n.42-1304C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290870	ENST00000647952.1	n.2156-1304C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39306 AN: 152010 Hom.: 5298 Cov.: 34

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.258 AC: 39314 AN: 152128 Hom.: 5301 Cov.: 34 AF XY: 0.257 AC XY: 19137 AN XY: 74364

African (AFR) AF: 0.191 AC: 7944 AN: 41518

American (AMR) AF: 0.236 AC: 3612 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1813 AN: 5154

South Asian (SAS) AF: 0.154 AC: 743 AN: 4828

European-Finnish (FIN) AF: 0.338 AC: 3572 AN: 10580

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20180 AN: 67968

Other (OTH) AF: 0.232 AC: 490 AN: 2112

Alfa AF: 0.277 Hom.: 821

Bravo AF: 0.252

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.76
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2734982; hg19: chr6-29821567;