7-41715041-A-T

Variant names:

• chr7-41715041-A-T
• rs7782324
• ENST00000415848.6:n.358+4259A>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+4259A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,974 control chromosomes in the GnomAD database, including 18,481 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 0.48 (18481 hom., cov: 32)
• Consequence: INHBA-AS1 ENST00000415848.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 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+4259A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INHBA-AS1	ENST00000415848.6	TSL:1	n.358+4259A>T		intron	N/A
	INHBA-AS1	ENST00000662248.1		n.280+4259A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73639 AN: 151856 Hom.: 18473 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.485 AC: 73657 AN: 151974 Hom.: 18481 Cov.: 32 AF XY: 0.487 AC XY: 36182 AN XY: 74280

African (AFR) AF: 0.384 AC: 15920 AN: 41414

American (AMR) AF: 0.387 AC: 5910 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1956 AN: 3462

East Asian (EAS) AF: 0.484 AC: 2498 AN: 5162

South Asian (SAS) AF: 0.490 AC: 2362 AN: 4820

European-Finnish (FIN) AF: 0.598 AC: 6308 AN: 10556

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37020 AN: 67972

Other (OTH) AF: 0.468 AC: 987 AN: 2110

Alfa AF: 0.395 Hom.: 1201

Bravo AF: 0.459

Asia WGS AF: 0.482 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.073

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: rs7782324;

hg19: chr7-41754639;