7-41720402-A-G

Position:

• chr7-41720402-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

INHBA-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INHBA-AS1	NR_027118.2	n.355+9620A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INHBA-AS1	ENST00000415848.6	n.358+9620A>G		intron_variant		1
INHBA-AS1	ENST00000662248.1	n.280+9620A>G		intron_variant

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

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.737

Alfa AF: 0.777 Hom.: 14892

Bravo AF: 0.736

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6463037; hg19: chr7-41760000;