rs3809114

Positions:

• chr12-57454856-G-A
• chr12-57454856-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000547970.1(INHBE):​n.154G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 454,126 control chromosomes in the GnomAD database, including 55,972 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 0.44 (16324 hom., cov: 33)
  • Exomes 𝑓: 0.50 (39648 hom.)
• Consequence: INHBE ENST00000547970.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

INHBE (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57454856G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INHBE	ENST00000551553.1	n.218-1238G>A		intron_variant		1
INHBE	ENST00000547970.1	n.154G>A		non_coding_transcript_exon_variant	1/3	3

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67208 AN: 152058 Hom.: 16321 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.479

GnomAD4 exome AF: 0.505 AC: 152349 AN: 301950 Hom.: 39648 Cov.: 0 AF XY: 0.502 AC XY: 86242 AN XY: 171956

Gnomad4 AFR exome AF: 0.235

Gnomad4 AMR exome AF: 0.463

Gnomad4 ASJ exome AF: 0.576

Gnomad4 EAS exome AF: 0.320

Gnomad4 SAS exome AF: 0.442

Gnomad4 FIN exome AF: 0.461

Gnomad4 NFE exome AF: 0.558

Gnomad4 OTH exome AF: 0.503

GnomAD4 genome AF: 0.442 AC: 67216 AN: 152176 Hom.: 16324 Cov.: 33 AF XY: 0.435 AC XY: 32385 AN XY: 74388

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.474

Alfa AF: 0.542 Hom.: 32979

Bravo AF: 0.439

Asia WGS AF: 0.338 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.031
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809114; hg19: chr12-57848639;