rs6439167

Variant names:

• chr3-129331913-T-C
• rs6439167
• ENST00000823125.1:n.194+13276T>C

Variant summary

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

The ENST00000823125.1(H1-10-AS1):​n.194+13276T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,190 control chromosomes in the GnomAD database, including 50,826 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 (50826 hom., cov: 32)
• Consequence: H1-10-AS1 ENST00000823125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 40 publications found

Genes affected

H1-10-AS1 (HGNC:27953): (H1-10 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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
H1-10-AS1	ENST00000823125.1	n.194+13276T>C		intron_variant	Intron 2 of 3
H1-10-AS1	ENST00000823130.1	n.147-14923T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124074 AN: 152072 Hom.: 50799 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.816 AC: 124159 AN: 152190 Hom.: 50826 Cov.: 32 AF XY: 0.817 AC XY: 60762 AN XY: 74410

African (AFR) AF: 0.859 AC: 35657 AN: 41522

American (AMR) AF: 0.798 AC: 12206 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2863 AN: 3472

East Asian (EAS) AF: 0.927 AC: 4799 AN: 5178

South Asian (SAS) AF: 0.828 AC: 3996 AN: 4826

European-Finnish (FIN) AF: 0.825 AC: 8738 AN: 10592

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53350 AN: 67992

Other (OTH) AF: 0.806 AC: 1704 AN: 2114

Alfa AF: 0.797 Hom.: 151845

Bravo AF: 0.815

Asia WGS AF: 0.844 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.32
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs6439167; hg19: chr3-129050756;