rs17776182

chr7-41718280-G-Achr7-41718280-G-C

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+7498G>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 0.133 in 152,152 control chromosomes in the GnomAD database, including 1,938 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 (1938 hom., cov: 32)
• Consequence: INHBA-AS1 NR_027118.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INHBA-AS1	NR_027118.2	n.355+7498G>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+7498G>A		intron_variant, non_coding_transcript_variant		1
INHBA-AS1	ENST00000662248.1	n.280+7498G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20230 AN: 152034 Hom.: 1935 Cov.: 32

Gnomad AFR AF: 0.0420

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.133 AC: 20228 AN: 152152 Hom.: 1938 Cov.: 32 AF XY: 0.140 AC XY: 10378 AN XY: 74392

Gnomad4 AFR AF: 0.0419

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.121

Alfa AF: 0.144 Hom.: 2442

Bravo AF: 0.122

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.90
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17776182; hg19: chr7-41757878;