ENST00000667164.1:n.2561A>G

Variant names:

• chr8-103244497-T-C
• rs4734695
• ENST00000667164.1:n.2561A>G

Variant summary

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

The ENST00000667164.1(BAALC-AS1):​n.2561A>G 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 0.368 in 152,038 control chromosomes in the GnomAD database, including 10,450 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 0.37 (10450 hom., cov: 32)
• Consequence: BAALC-AS1 ENST00000667164.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

BAALC-AS1 (HGNC:50461): (BAALC antisense RNA 1)

LOC105369147 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369147	NR_148213.1	n.2767A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105369147	NR_148216.1	n.2658A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAALC-AS1	ENST00000667164.1	n.2561A>G		non_coding_transcript_exon_variant	Exon 2 of 2
BAALC-AS1	ENST00000499522.6	n.892+1797A>G		intron_variant	Intron 4 of 5	5
BAALC-AS1	ENST00000523614.6	n.99+41341A>G		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55834 AN: 151920 Hom.: 10432 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.368 AC: 55896 AN: 152038 Hom.: 10450 Cov.: 32 AF XY: 0.366 AC XY: 27164 AN XY: 74312

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.375

Alfa AF: 0.382 Hom.: 17327

Bravo AF: 0.369

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
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: rs4734695; hg19: chr8-104256725;