7-41720402-A-G

Variant names:

• chr7-41720402-A-G
• rs6463037
• ENST00000415848.6:n.358+9620A>G

Variant summary

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

The ENST00000415848.6(INHBA-AS1):​n.358+9620A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,212 control chromosomes in the GnomAD database, including 44,638 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 0.76 (44638 hom., cov: 33)
• Consequence: INHBA-AS1 ENST00000415848.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 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.355+9620A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	ENST00000415848.6	TSL:1	n.358+9620A>G		intron	N/A
	INHBA-AS1	ENST00000662248.1		n.280+9620A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115979 AN: 152094 Hom.: 44612 Cov.: 33

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.762 AC: 116052 AN: 152212 Hom.: 44638 Cov.: 33 AF XY: 0.764 AC XY: 56904 AN XY: 74440

African (AFR) AF: 0.720 AC: 29897 AN: 41506

American (AMR) AF: 0.630 AC: 9636 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2608 AN: 3470

East Asian (EAS) AF: 0.752 AC: 3890 AN: 5170

South Asian (SAS) AF: 0.737 AC: 3548 AN: 4814

European-Finnish (FIN) AF: 0.882 AC: 9361 AN: 10616

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54516 AN: 68020

Other (OTH) AF: 0.737 AC: 1559 AN: 2116

Alfa AF: 0.774 Hom.: 18281

Bravo AF: 0.736

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.44
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs6463037; hg19: chr7-41760000;