7-41737279-G-T

Variant names:

• chr7-41737279-G-T
• rs10951655
• ENST00000415848.6:n.358+26497G>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.358+26497G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,118 control chromosomes in the GnomAD database, including 40,181 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 0.72 (40181 hom., cov: 33)
• Consequence: INHBA-AS1 ENST00000415848.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 1 publications found

Genes affected

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

ENSG00000309263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INHBA-AS1	NR_027118.2	n.355+26497G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INHBA-AS1	ENST00000415848.6	n.358+26497G>T		intron_variant	Intron 2 of 3	1
INHBA-AS1	ENST00000662248.1	n.280+26497G>T		intron_variant	Intron 2 of 2
ENSG00000309263	ENST00000839902.1	n.452+1575G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108900 AN: 152000 Hom.: 40183 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.716 AC: 108927 AN: 152118 Hom.: 40181 Cov.: 33 AF XY: 0.719 AC XY: 53449 AN XY: 74386

African (AFR) AF: 0.543 AC: 22488 AN: 41430

American (AMR) AF: 0.613 AC: 9373 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2635 AN: 3470

East Asian (EAS) AF: 0.749 AC: 3876 AN: 5176

South Asian (SAS) AF: 0.731 AC: 3518 AN: 4814

European-Finnish (FIN) AF: 0.885 AC: 9391 AN: 10612

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55113 AN: 68016

Other (OTH) AF: 0.706 AC: 1491 AN: 2112

Alfa AF: 0.745 Hom.: 16794

Bravo AF: 0.684

Asia WGS AF: 0.708 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10951655; hg19: chr7-41776877;