rs998190

Positions:

• chr7-41710184-G-A
• chr7-41710184-G-C
• chr7-41710184-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.171-414G>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 0.131 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 NR_027118.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INHBA-AS1	NR_027118.2	n.171-414G>A		intron_variant, non_coding_transcript_variant
INHBA-AS1	NR_027119.2	n.171-414G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INHBA-AS1	ENST00000415848.6	n.174-414G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.0358

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.126

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs998190; hg19: chr7-41749782;