rs10016388

Variant names:

• chr4-47161613-A-C
• rs10016388
• NM_000812.4:c.461+144A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-47161613-A-C
• chr4-47161613-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000812.4(GABRB1):​c.461+144A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000021 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GABRB1 NM_000812.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 0 publications found

Genes affected

GABRB1 (HGNC:4081): (gamma-aminobutyric acid type A receptor subunit beta1) The gamma-aminobutyric acid (GABA) A receptor is a multisubunit chloride channel that mediates the fastest inhibitory synaptic transmission in the central nervous system. This gene encodes GABA A receptor, beta 1 subunit. It is mapped to chromosome 4p12 in a cluster comprised of genes encoding alpha 4, alpha 2 and gamma 1 subunits of the GABA A receptor. Alteration of this gene is implicated in the pathogenetics of schizophrenia. [provided by RefSeq, Jul 2008]

GABRB1 Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy, 45

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRB1	NM_000812.4	c.461+144A>C		intron_variant	Intron 4 of 8	ENST00000295454.8	NP_000803.2
GABRB1	XM_024453976.2	c.362+144A>C		intron_variant	Intron 4 of 8		XP_024309744.1
GABRB1	XM_024453977.2	c.362+144A>C		intron_variant	Intron 5 of 9		XP_024309745.1
GABRB1	XM_017007986.3	c.461+144A>C		intron_variant	Intron 4 of 4		XP_016863475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRB1	ENST00000295454.8	c.461+144A>C		intron_variant	Intron 4 of 8	1	NM_000812.4	ENSP00000295454.3
GABRB1	ENST00000510909.1	n.*129+144A>C		intron_variant	Intron 3 of 4	4		ENSP00000426766.1
GABRB1	ENST00000513567.5	c.*153A>C		downstream_gene_variant		4		ENSP00000426753.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000209 AC: 1 AN: 477380 Hom.: 0 AF XY: 0.00000398 AC XY: 1 AN XY: 251360

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 12770

American (AMR) AF: 0.00 AC: 0 AN: 18248

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13660

East Asian (EAS) AF: 0.00 AC: 0 AN: 30982

South Asian (SAS) AF: 0.00 AC: 0 AN: 45276

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30372

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1998

European-Non Finnish (NFE) AF: 0.00000336 AC: 1 AN: 297428

Other (OTH) AF: 0.00 AC: 0 AN: 26646

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 2801

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.30
PhyloP100		0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10016388; hg19: chr4-47163630;