rs4713240

Positions:

• chr6-29742949-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026973.1(HLA-F-AS1):​n.150+5951T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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: HLA-F-AS1 NR_026973.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-F-AS1	NR_026973.1	n.150+5951T>C		intron_variant, non_coding_transcript_variant
HLA-F-AS1	NR_026972.1	n.429-4063T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICE	ENST00000510438.1	n.1032+1060T>C		intron_variant, non_coding_transcript_variant
HLA-F-AS1	ENST00000458236.1	n.349+2524T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.200

Alfa AF: 0.238 Hom.: 5401

Bravo AF: 0.227

Asia WGS AF: 0.236 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713240; hg19: chr6-29710726;