8-121642411-A-T

Variant names:

• chr8-121642411-A-T
• rs4123220
• ENST00000514180.6:n.1081-173A>T

Variant summary

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

The ENST00000514180.6(HAS2-AS1):​n.1081-173A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,894 control chromosomes in the GnomAD database, including 15,020 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 0.41 (15020 hom., cov: 31)
• Consequence: HAS2-AS1 ENST00000514180.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 1 publications found

Genes affected

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

ENSG00000295139 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAS2-AS1	NR_002835.2	n.1081-173A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAS2-AS1	ENST00000514180.6	n.1081-173A>T		intron_variant	Intron 2 of 3	1
ENSG00000295139	ENST00000728224.1	n.369T>A		non_coding_transcript_exon_variant	Exon 2 of 2
HAS2-AS1	ENST00000518865.6	n.351-173A>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61844 AN: 151774 Hom.: 14980 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.408 AC: 61940 AN: 151894 Hom.: 15020 Cov.: 31 AF XY: 0.412 AC XY: 30583 AN XY: 74252

African (AFR) AF: 0.644 AC: 26701 AN: 41436

American (AMR) AF: 0.427 AC: 6517 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3707 AN: 5120

South Asian (SAS) AF: 0.368 AC: 1768 AN: 4808

European-Finnish (FIN) AF: 0.328 AC: 3470 AN: 10566

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17712 AN: 67930

Other (OTH) AF: 0.396 AC: 834 AN: 2104

Alfa AF: 0.163 Hom.: 287

Bravo AF: 0.426

Asia WGS AF: 0.567 AC: 1972 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	7.3
DANN	Benign	0.73
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs4123220; hg19: chr8-122654651;