rs113795410

Variant names:

• chr6-29760432-C-A
• rs113795410
• ENST00000648999.2:n.356-1342C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29760432-C-A
• chr6-29760432-C-G
• chr6-29760432-C-T

Variant summary

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

The ENST00000648999.2(ENSG00000285761):​n.356-1342C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,186 control chromosomes in the GnomAD database, including 51,080 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 0.82 (51080 hom., cov: 32)
• Consequence: ENSG00000285761 ENST00000648999.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648999.2. 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
	ENSG00000285761	ENST00000648999.2		n.356-1342C>A		intron	N/A
	HLA-F-AS1	ENST00000849873.1		n.421+31675G>T		intron	N/A
	HLA-F-AS1	ENST00000849874.1		n.403+31675G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124188 AN: 152068 Hom.: 51019 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.817 AC: 124308 AN: 152186 Hom.: 51080 Cov.: 32 AF XY: 0.815 AC XY: 60617 AN XY: 74390

African (AFR) AF: 0.790 AC: 32770 AN: 41492

American (AMR) AF: 0.867 AC: 13265 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3036 AN: 3470

East Asian (EAS) AF: 0.983 AC: 5094 AN: 5180

South Asian (SAS) AF: 0.928 AC: 4484 AN: 4830

European-Finnish (FIN) AF: 0.690 AC: 7299 AN: 10580

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55600 AN: 68010

Other (OTH) AF: 0.825 AC: 1743 AN: 2114

Alfa AF: 0.827 Hom.: 127575

Bravo AF: 0.828

Asia WGS AF: 0.939 AC: 3267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-0.55

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: rs113795410;

hg19: chr6-29728209;