Genetic Variant HAS2-AS1:n.315-7175C>T (chr8-121896264-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000523550.1(HAS2-AS1):n.315-7175C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,918 control chromosomes in the GnomAD database, including 14,967 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 0.39 ( 14967 hom., cov: 31)

Consequence

HAS2-AS1
ENST00000523550.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.07

Variant links:

Genes affected

HAS2-AS1 (HGNC:34340): (HAS2 antisense RNA 1)

HAS2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HAS2-AS1	ENST00000523550.1 link	n.315-7175C>T	intron_variant	Intron 2 of 3	3
HAS2-AS1	ENST00000647560.1 link	n.446+16499C>T	intron_variant	Intron 3 of 3
HAS2-AS1	ENST00000648171.1 link	n.969-7175C>T	intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59588

AN:

151800

Hom.:

14968

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.385

Gnomad ASJ

AF:

0.437

Gnomad EAS

AF:

0.0968

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.542

Gnomad MID

AF:

0.414

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.420

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

GnomAD4 genome

AF:

0.392

AC:

59574

AN:

151918

Hom.:

14967

Cov.:

AF XY:

0.387

AC XY:

28763

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.385

Gnomad4 ASJ

AF:

0.437

Gnomad4 EAS

AF:

0.0966

Gnomad4 SAS

AF:

0.324

Gnomad4 FIN

AF:

0.542

Gnomad4 NFE

AF:

0.570

Gnomad4 OTH

AF:

0.414

Alfa

AF:

0.521

Hom.:

36952

Bravo

AF:

0.367

Asia WGS

AF:

0.194

AC:

678

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.13

DANN

Benign

0.73

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over