chr8-121896264-C-T

Variant names:

• chr8-121896264-C-T
• rs7844723
• ENST00000523550.1:n.315-7175C>T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523550.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAS2-AS1	ENST00000523550.1	TSL:3	n.315-7175C>T		intron	N/A
	HAS2-AS1	ENST00000647560.2		n.446+16499C>T		intron	N/A
	HAS2-AS1	ENST00000648171.1		n.969-7175C>T		intron	N/A

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

African (AFR) AF: 0.101 AC: 4192 AN: 41492

American (AMR) AF: 0.385 AC: 5867 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1517 AN: 3472

East Asian (EAS) AF: 0.0966 AC: 499 AN: 5164

South Asian (SAS) AF: 0.324 AC: 1563 AN: 4822

European-Finnish (FIN) AF: 0.542 AC: 5699 AN: 10522

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.570 AC: 38659 AN: 67882

Other (OTH) AF: 0.414 AC: 873 AN: 2110

Alfa AF: 0.493 Hom.: 55424

Bravo AF: 0.367

Asia WGS AF: 0.194 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.13
DANN	Benign	0.73
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7844723; hg19: chr8-122908503;