chr6-29825947-T-C

Variant names:

• chr6-29825947-T-C
• rs1632949
• ENST00000849927.1:n.26+2524A>G

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+2524A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,964 control chromosomes in the GnomAD database, including 8,923 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 0.34 (8923 hom., cov: 31)
• Consequence: HLA-F-AS1 ENST00000849927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 16 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 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+2524A>G		intron	N/A
	HLA-F-AS1	ENST00000849935.1		n.230+1773A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51561 AN: 151844 Hom.: 8913 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.340 AC: 51603 AN: 151964 Hom.: 8923 Cov.: 31 AF XY: 0.337 AC XY: 25056 AN XY: 74280

African (AFR) AF: 0.286 AC: 11855 AN: 41422

American (AMR) AF: 0.340 AC: 5191 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3466

East Asian (EAS) AF: 0.306 AC: 1581 AN: 5168

South Asian (SAS) AF: 0.462 AC: 2226 AN: 4820

European-Finnish (FIN) AF: 0.252 AC: 2662 AN: 10562

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25318 AN: 67942

Other (OTH) AF: 0.347 AC: 731 AN: 2106

Alfa AF: 0.358 Hom.: 6915

Bravo AF: 0.341

Asia WGS AF: 0.355 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.41
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1632949; hg19: chr6-29793724;