chr14-100565880-T-C

Variant names:

• chr14-100565880-T-C
• rs6575793
• NM_001385089.1:c.71+2031A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001385089.1(BEGAIN):​c.71+2031A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,166 control chromosomes in the GnomAD database, including 24,918 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 0.54 (24918 hom., cov: 33)
• Consequence: BEGAIN NM_001385089.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900

Genes affected

BEGAIN (HGNC:24163): (brain enriched guanylate kinase associated) Predicted to be involved in regulation of postsynaptic neurotransmitter receptor activity. Predicted to act upstream of or within evoked excitatory postsynaptic potential. Predicted to be located in dendrite; nucleus; and presynapse. Predicted to be active in glutamatergic synapse and postsynapse. [provided by Alliance of Genome Resources, Apr 2022]

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 (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BEGAIN	NM_001385089.1	c.71+2031A>G		intron_variant	Intron 2 of 6	ENST00000554140.3	NP_001372018.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BEGAIN	ENST00000554140.3	c.71+2031A>G		intron_variant	Intron 2 of 6	5	NM_001385089.1	ENSP00000451125.2

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82730 AN: 152048 Hom.: 24851 Cov.: 33

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.545 AC: 82865 AN: 152166 Hom.: 24918 Cov.: 33 AF XY: 0.545 AC XY: 40512 AN XY: 74372

African (AFR) AF: 0.809 AC: 33569 AN: 41516

American (AMR) AF: 0.557 AC: 8509 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3468

East Asian (EAS) AF: 0.660 AC: 3414 AN: 5176

South Asian (SAS) AF: 0.482 AC: 2327 AN: 4828

European-Finnish (FIN) AF: 0.446 AC: 4729 AN: 10592

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27491 AN: 67984

Other (OTH) AF: 0.503 AC: 1060 AN: 2108

Alfa AF: 0.429 Hom.: 26920

Bravo AF: 0.565

Asia WGS AF: 0.573 AC: 1992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.60
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

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

Publications

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Other links and lift over

dbSNP: rs6575793; hg19: chr14-101032217;