rs4734695

Variant names:

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

Variant summary

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

The NR_148213.1(LOC105369147):​n.2767A>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: LOC105369147 NR_148213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 6 publications found

Genes affected

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

LOC105369147 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_148213.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105369147	NR_148213.1		n.2767A>G		non_coding_transcript_exon	Exon 4 of 4
	LOC105369147	NR_148216.1		n.2658A>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAALC-AS1	ENST00000667164.1		n.2561A>G		non_coding_transcript_exon	Exon 2 of 2
	BAALC-AS1	ENST00000499522.6	TSL:5	n.892+1797A>G		intron	N/A
	BAALC-AS1	ENST00000523614.6	TSL:5	n.99+41341A>G		intron	N/A

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

African (AFR) AF: 0.373 AC: 15492 AN: 41480

American (AMR) AF: 0.337 AC: 5154 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1503 AN: 5158

South Asian (SAS) AF: 0.363 AC: 1750 AN: 4820

European-Finnish (FIN) AF: 0.347 AC: 3666 AN: 10564

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25278 AN: 67952

Other (OTH) AF: 0.375 AC: 791 AN: 2112

Alfa AF: 0.380 Hom.: 20954

Bravo AF: 0.369

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.49
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4734695;

hg19: chr8-104256725;