rs17719440

chr7-41715345-C-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+4563C>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 0.058 in 152,270 control chromosomes in the GnomAD database, including 280 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 0.058 (280 hom., cov: 32)
• Consequence: INHBA-AS1 NR_027118.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775

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 (AMR) allele frequency at 95% confidence interval = 0.0724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INHBA-AS1	NR_027118.2	n.355+4563C>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+4563C>T		intron_variant, non_coding_transcript_variant		1
INHBA-AS1	ENST00000662248.1	n.280+4563C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0580 AC: 8825 AN: 152150 Hom.: 280 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.0493

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0741

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0580 AC: 8825 AN: 152270 Hom.: 280 Cov.: 32 AF XY: 0.0563 AC XY: 4192 AN XY: 74456

Gnomad4 AFR AF: 0.0304

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.0542

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0741

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0650 Hom.: 96

Bravo AF: 0.0587

Asia WGS AF: 0.0480 AC: 165 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	0.21
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17719440; hg19: chr7-41754943;