rs720816

chr7-41736150-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027118.2(INHBA-AS1):n.355+25368G>A variant causes a intron, non coding transcript 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 NR_027118.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
INHBA-AS1	NR_027118.2	n.355+25368G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INHBA-AS1	ENST00000415848.6	n.358+25368G>A		intron_variant, non_coding_transcript_variant		1
INHBA-AS1	ENST00000662248.1	n.280+25368G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.443

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720816; hg19: chr7-41775748;