rs7844723

chr8-121896264-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664717.1(HAS2-AS1):n.959+7287C>T variant causes a intron, non coding transcript 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 ENST00000664717.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

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

ACMG classification

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HAS2-AS1	ENST00000664717.1	n.959+7287C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59588 AN: 151800 Hom.: 14968 Cov.: 31

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.: 31 AF XY: 0.387 AC XY: 28763 AN XY: 74240

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

Other links and lift over

dbSNP: rs7844723; hg19: chr8-122908503;