rs10486722

Positions:

• chr7-41772310-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.356-586C>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 0.593 in 152,054 control chromosomes in the GnomAD database, including 27,515 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 0.59 (27515 hom., cov: 32)
• Consequence: INHBA-AS1 NR_027118.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INHBA-AS1	NR_027118.2	n.356-586C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INHBA-AS1	ENST00000415848.6	n.359-586C>T		intron_variant, non_coding_transcript_variant		1
INHBA-AS1	ENST00000662248.1	n.281-4531C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90147 AN: 151936 Hom.: 27508 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.593 AC: 90183 AN: 152054 Hom.: 27515 Cov.: 32 AF XY: 0.591 AC XY: 43966 AN XY: 74332

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.587

Alfa AF: 0.648 Hom.: 42985

Bravo AF: 0.570

Asia WGS AF: 0.539 AC: 1874 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486722; hg19: chr7-41811908;