chr6-29819295-C-T

Variant names:

• chr6-29819295-C-T
• rs2743931
• ENST00000849927.1:n.26+9176G>A

Variant summary

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

The ENST00000849927.1(HLA-F-AS1):​n.26+9176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,212 control chromosomes in the GnomAD database, including 59,328 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 0.88 (59328 hom., cov: 32)
• Consequence: HLA-F-AS1 ENST00000849927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 13 publications found

Genes affected

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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849927.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	ENST00000849927.1		n.26+9176G>A		intron	N/A
	HLA-F-AS1	ENST00000849935.1		n.230+8425G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133885 AN: 152094 Hom.: 59258 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.880 AC: 134014 AN: 152212 Hom.: 59328 Cov.: 32 AF XY: 0.877 AC XY: 65222 AN XY: 74384

African (AFR) AF: 0.930 AC: 38639 AN: 41540

American (AMR) AF: 0.917 AC: 14020 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3137 AN: 3468

East Asian (EAS) AF: 0.986 AC: 5113 AN: 5184

South Asian (SAS) AF: 0.938 AC: 4532 AN: 4830

European-Finnish (FIN) AF: 0.726 AC: 7672 AN: 10568

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57972 AN: 68008

Other (OTH) AF: 0.893 AC: 1885 AN: 2112

Alfa AF: 0.876 Hom.: 53529

Bravo AF: 0.898

Asia WGS AF: 0.961 AC: 3343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.44
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2743931; hg19: chr6-29787072;