6-29757162-G-T

Variant names:

• chr6-29757162-G-T
• rs1737078
• ENST00000850393.1:n.1067G>T

Variant summary

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

The ENST00000850393.1(ENSG00000285761):​n.1067G>T 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 0.448 in 151,952 control chromosomes in the GnomAD database, including 15,406 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 0.45 (15406 hom., cov: 32)
• Consequence: ENSG00000285761 ENST00000850393.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 22 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.522 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	ENST00000850393.1	n.1067G>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000285761	ENST00000648999.2	n.355+4235G>T		intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849873.1	n.422-30023C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67992 AN: 151834 Hom.: 15381 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.448 AC: 68061 AN: 151952 Hom.: 15406 Cov.: 32 AF XY: 0.444 AC XY: 32956 AN XY: 74286

African (AFR) AF: 0.435 AC: 17998 AN: 41422

American (AMR) AF: 0.532 AC: 8116 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1650 AN: 5166

South Asian (SAS) AF: 0.444 AC: 2134 AN: 4810

European-Finnish (FIN) AF: 0.321 AC: 3390 AN: 10564

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.460 AC: 31242 AN: 67944

Other (OTH) AF: 0.487 AC: 1026 AN: 2108

Alfa AF: 0.467 Hom.: 52613

Bravo AF: 0.462

Asia WGS AF: 0.473 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.31
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1737078; hg19: chr6-29724939;