rs4713240

Variant names:

• chr6-29742949-A-G
• rs4713240

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 0.232 in 152,264 control chromosomes in the GnomAD database, including 4,137 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 0.23 (4137 hom., cov: 34)
• Consequence: MICE intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 30 publications found

Genes affected

MICE (HGNC:7094): (MHC class I polypeptide-related sequence E (pseudogene))

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399247.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	NR_026972.1		n.429-4063T>C		intron	N/A
	HLA-F-AS1	NR_026973.1		n.150+5951T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	ENST00000399247.6	TSL:6	n.429-4063T>C		intron	N/A
	HLA-F-AS1	ENST00000434086.2	TSL:6	n.354-4063T>C		intron	N/A
	HLA-F-AS1	ENST00000458236.1	TSL:6	n.349+2524T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35294 AN: 152146 Hom.: 4127 Cov.: 34

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.232 AC: 35327 AN: 152264 Hom.: 4137 Cov.: 34 AF XY: 0.233 AC XY: 17318 AN XY: 74452

African (AFR) AF: 0.206 AC: 8574 AN: 41540

American (AMR) AF: 0.202 AC: 3094 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 637 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1938 AN: 5178

South Asian (SAS) AF: 0.182 AC: 878 AN: 4826

European-Finnish (FIN) AF: 0.282 AC: 2989 AN: 10606

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

European-Non Finnish (NFE) AF: 0.243 AC: 16500 AN: 68014

Other (OTH) AF: 0.200 AC: 424 AN: 2116

Alfa AF: 0.239 Hom.: 14617

Bravo AF: 0.227

Asia WGS AF: 0.236 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.90
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs4713240; hg19: chr6-29710726;