chr6-29747555-C-A

Position:

• chr6-29747555-C-A

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+1345G>T 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 0.224 in 151,346 control chromosomes in the GnomAD database, including 3,887 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 0.22 (3870 hom., cov: 28)
  • Exomes 𝑓: 0.25 (17 hom.)
• Consequence: HLA-F-AS1 NR_026973.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 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+1345G>T		intron_variant, non_coding_transcript_variant
HLA-F-AS1	NR_026972.1	n.151-130G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICE	ENST00000510438.1	n.70+1345G>T		intron_variant, non_coding_transcript_variant
HLA-F-AS1	ENST00000458236.1	n.94+1345G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33817 AN: 150782 Hom.: 3869 Cov.: 28

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.187

GnomAD4 exome AF: 0.247 AC: 111 AN: 450 Hom.: 17 AF XY: 0.242 AC XY: 72 AN XY: 298

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.107

Gnomad4 FIN exome AF: 0.344

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.262

GnomAD4 genome AF: 0.224 AC: 33827 AN: 150896 Hom.: 3870 Cov.: 28 AF XY: 0.225 AC XY: 16568 AN XY: 73674

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.186

Alfa AF: 0.236 Hom.: 2579

Bravo AF: 0.218

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.50
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34260811; hg19: chr6-29715332;