rs4713244

Variant names:

• chr6-29753369-G-A
• rs4713244
• ENST00000850396.1:n.658G>A

Variant summary

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

The ENST00000850396.1(ENSG00000285761):​n.658G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 141,098 control chromosomes in the GnomAD database, including 3,031 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 0.20 (3031 hom., cov: 23)
• Consequence: ENSG00000285761 ENST00000850396.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 12 publications found

Genes affected

ENSG00000285761 (HGNC:):

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285761	ENST00000850396.1	n.658G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000285761	ENST00000648999.2	n.355+442G>A		intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849873.1	n.422-26230C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 28120 AN: 140976 Hom.: 3030 Cov.: 23

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.199 AC: 28132 AN: 141098 Hom.: 3031 Cov.: 23 AF XY: 0.198 AC XY: 13522 AN XY: 68384

African (AFR) AF: 0.151 AC: 5728 AN: 37952

American (AMR) AF: 0.171 AC: 2397 AN: 14040

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 610 AN: 3398

East Asian (EAS) AF: 0.339 AC: 1557 AN: 4594

South Asian (SAS) AF: 0.133 AC: 591 AN: 4432

European-Finnish (FIN) AF: 0.244 AC: 2170 AN: 8910

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 14529 AN: 64696

Other (OTH) AF: 0.155 AC: 297 AN: 1920

Alfa AF: 0.229 Hom.: 9395

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.66
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs4713244; hg19: chr6-29721146;