rs1003291

Variant names:

• chr7-41710489-G-A
• rs1003291
• ENST00000415848.6:n.174-109G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-41710489-G-A
• chr7-41710489-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415848.6(INHBA-AS1):​n.174-109G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,260 control chromosomes in the GnomAD database, including 52,619 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 0.83 (52618 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: INHBA-AS1 ENST00000415848.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 4 publications found

Genes affected

INHBA-AS1 (HGNC:40303): (INHBA antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415848.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	NR_027118.2		n.171-109G>A		intron	N/A
	INHBA-AS1	NR_027119.2		n.171-109G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	ENST00000415848.6	TSL:1	n.174-109G>A		intron	N/A
	INHBA-AS1	ENST00000420821.2	TSL:1	n.161-109G>A		intron	N/A
	INHBA-AS1	ENST00000422822.1	TSL:2	n.153-109G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125651 AN: 152140 Hom.: 52569 Cov.: 33

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.786

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.826 AC: 125750 AN: 152258 Hom.: 52618 Cov.: 33 AF XY: 0.825 AC XY: 61433 AN XY: 74450

African (AFR) AF: 0.939 AC: 39018 AN: 41566

American (AMR) AF: 0.653 AC: 9975 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2608 AN: 3466

East Asian (EAS) AF: 0.755 AC: 3909 AN: 5178

South Asian (SAS) AF: 0.740 AC: 3572 AN: 4826

European-Finnish (FIN) AF: 0.882 AC: 9361 AN: 10608

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54602 AN: 68010

Other (OTH) AF: 0.787 AC: 1663 AN: 2112

Alfa AF: 0.792 Hom.: 85781

Bravo AF: 0.810

Asia WGS AF: 0.749 AC: 2604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1003291;

hg19: chr7-41750087;