rs13151769

Positions:

• chr4-46993643-G-A
• chr4-46993643-G-C

Variant summary

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

The 4-46993643-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 568,026 control chromosomes in the GnomAD database, including 32,087 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 0.34 (8743 hom., cov: 32)
  • Exomes 𝑓: 0.33 (23344 hom.)
• Consequence: GABRB1 XM_024453976.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

Genes affected

GABRB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRB1	XM_024453976.2			upstream_gene_variant
GABRB1	XM_024453977.2			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50891 AN: 151772 Hom.: 8720 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.346

GnomAD4 exome AF: 0.329 AC: 136933 AN: 416136 Hom.: 23344 Cov.: 3 AF XY: 0.322 AC XY: 71075 AN XY: 220470

Gnomad4 AFR exome AF: 0.347

Gnomad4 AMR exome AF: 0.304

Gnomad4 ASJ exome AF: 0.387

Gnomad4 EAS exome AF: 0.323

Gnomad4 SAS exome AF: 0.213

Gnomad4 FIN exome AF: 0.234

Gnomad4 NFE exome AF: 0.358

Gnomad4 OTH exome AF: 0.340

GnomAD4 genome AF: 0.335 AC: 50957 AN: 151890 Hom.: 8743 Cov.: 32 AF XY: 0.324 AC XY: 24040 AN XY: 74206

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.348

Alfa AF: 0.317 Hom.: 944

Bravo AF: 0.350

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13151769; hg19: chr4-46995660;