rs10486722

Variant names:

• chr7-41772310-C-T
• rs10486722
• ENST00000415848.6:n.359-586C>T

Variant summary

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

The ENST00000415848.6(INHBA-AS1):​n.359-586C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,054 control chromosomes in the GnomAD database, including 27,515 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 0.59 (27515 hom., cov: 32)
• Consequence: INHBA-AS1 ENST00000415848.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 8 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415848.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	NR_027118.2		n.356-586C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	ENST00000415848.6	TSL:1	n.359-586C>T		intron	N/A
	INHBA-AS1	ENST00000662248.1		n.281-4531C>T		intron	N/A
	ENSG00000309263	ENST00000839902.1		n.452+36606C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90147 AN: 151936 Hom.: 27508 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.593 AC: 90183 AN: 152054 Hom.: 27515 Cov.: 32 AF XY: 0.591 AC XY: 43966 AN XY: 74332

African (AFR) AF: 0.477 AC: 19782 AN: 41470

American (AMR) AF: 0.502 AC: 7671 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2367 AN: 3470

East Asian (EAS) AF: 0.494 AC: 2556 AN: 5170

South Asian (SAS) AF: 0.571 AC: 2757 AN: 4826

European-Finnish (FIN) AF: 0.671 AC: 7081 AN: 10546

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45890 AN: 67990

Other (OTH) AF: 0.587 AC: 1238 AN: 2108

Alfa AF: 0.639 Hom.: 94228

Bravo AF: 0.570

Asia WGS AF: 0.539 AC: 1874 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.19
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10486722;

hg19: chr7-41811908;