ENST00000415848.6:n.174-414G>A

Variant names:

• chr7-41710184-G-A
• rs998190
• ENST00000415848.6:n.174-414G>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.174-414G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,086 control chromosomes in the GnomAD database, including 1,685 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 0.13 (1685 hom., cov: 33)
• Consequence: INHBA-AS1 ENST00000415848.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	NR_027118.2		n.171-414G>A		intron	N/A
	INHBA-AS1	NR_027119.2		n.171-414G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	ENST00000415848.6	TSL:1	n.174-414G>A		intron	N/A
	INHBA-AS1	ENST00000420821.2	TSL:1	n.161-414G>A		intron	N/A
	INHBA-AS1	ENST00000422822.1	TSL:2	n.153-414G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19946 AN: 151968 Hom.: 1684 Cov.: 33

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.131 AC: 19938 AN: 152086 Hom.: 1685 Cov.: 33 AF XY: 0.134 AC XY: 9958 AN XY: 74352

African (AFR) AF: 0.0358 AC: 1484 AN: 41484

American (AMR) AF: 0.103 AC: 1580 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 394 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1005 AN: 5154

South Asian (SAS) AF: 0.182 AC: 876 AN: 4812

European-Finnish (FIN) AF: 0.229 AC: 2429 AN: 10590

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11667 AN: 67974

Other (OTH) AF: 0.126 AC: 266 AN: 2108

Alfa AF: 0.124 Hom.: 400

Bravo AF: 0.116

Asia WGS AF: 0.149 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.53
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs998190; hg19: chr7-41749782;