7-41737279-G-T

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+26497G>T 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 0.716 in 152,118 control chromosomes in the GnomAD database, including 40,181 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 0.72 (40181 hom., cov: 33)
• Consequence: INHBA-AS1 NR_027118.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INHBA-AS1	NR_027118.2	n.355+26497G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INHBA-AS1	ENST00000415848.6	n.358+26497G>T		intron_variant, non_coding_transcript_variant		1
INHBA-AS1	ENST00000662248.1	n.280+26497G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108900 AN: 152000 Hom.: 40183 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.716 AC: 108927 AN: 152118 Hom.: 40181 Cov.: 33 AF XY: 0.719 AC XY: 53449 AN XY: 74386

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.706

Alfa AF: 0.747 Hom.: 9552

Bravo AF: 0.684

Asia WGS AF: 0.708 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.35
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10951655; hg19: chr7-41776877;