6-29768270-T-C

Variant names:

• chr6-29768270-T-C
• rs1737043
• ENST00000849873.1:n.421+23837A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000849873.1(HLA-F-AS1):​n.421+23837A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 151,954 control chromosomes in the GnomAD database, including 41,327 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 0.73 (41327 hom., cov: 33)
• Consequence: HLA-F-AS1 ENST00000849873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 18 publications found

Genes affected

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

ENSG00000285761 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849873.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	ENST00000849873.1		n.421+23837A>G		intron	N/A
	HLA-F-AS1	ENST00000849874.1		n.403+23837A>G		intron	N/A
	HLA-F-AS1	ENST00000849875.1		n.354+23837A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111006 AN: 151838 Hom.: 41283 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.731 AC: 111093 AN: 151954 Hom.: 41327 Cov.: 33 AF XY: 0.721 AC XY: 53558 AN XY: 74300

African (AFR) AF: 0.854 AC: 35354 AN: 41404

American (AMR) AF: 0.719 AC: 10974 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2611 AN: 3468

East Asian (EAS) AF: 0.567 AC: 2926 AN: 5164

South Asian (SAS) AF: 0.593 AC: 2853 AN: 4810

European-Finnish (FIN) AF: 0.581 AC: 6135 AN: 10568

Middle Eastern (MID) AF: 0.731 AC: 212 AN: 290

European-Non Finnish (NFE) AF: 0.706 AC: 47958 AN: 67962

Other (OTH) AF: 0.727 AC: 1532 AN: 2108

Alfa AF: 0.718 Hom.: 152787

Bravo AF: 0.753

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.35
PhyloP100		-2.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1737043;

hg19: chr6-29736047;