rs720816

Variant names:

• chr7-41736150-G-A
• rs720816
• ENST00000415848.6:n.358+25368G>A

Variant summary

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

The ENST00000415848.6(INHBA-AS1):​n.358+25368G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,034 control chromosomes in the GnomAD database, including 16,908 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 0.46 (16908 hom., cov: 32)
• Consequence: INHBA-AS1 ENST00000415848.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 5 publications found

Genes affected

INHBA-AS1 (HGNC:40303): (INHBA antisense RNA 1)

ENSG00000309263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INHBA-AS1	NR_027118.2	n.355+25368G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INHBA-AS1	ENST00000415848.6	n.358+25368G>A		intron_variant	Intron 2 of 3	1
INHBA-AS1	ENST00000662248.1	n.280+25368G>A		intron_variant	Intron 2 of 2
ENSG00000309263	ENST00000839902.1	n.452+446G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69303 AN: 151916 Hom.: 16905 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.456 AC: 69311 AN: 152034 Hom.: 16908 Cov.: 32 AF XY: 0.460 AC XY: 34144 AN XY: 74288

African (AFR) AF: 0.291 AC: 12064 AN: 41458

American (AMR) AF: 0.380 AC: 5804 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1957 AN: 3472

East Asian (EAS) AF: 0.474 AC: 2447 AN: 5160

South Asian (SAS) AF: 0.496 AC: 2387 AN: 4812

European-Finnish (FIN) AF: 0.586 AC: 6186 AN: 10558

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36857 AN: 67968

Other (OTH) AF: 0.443 AC: 934 AN: 2110

Alfa AF: 0.485 Hom.: 3253

Bravo AF: 0.429

Asia WGS AF: 0.480 AC: 1670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs720816; hg19: chr7-41775748;