rs3107646

Variant names:

• chr8-103273303-G-A
• rs3107646
• ENST00000499522.6:n.71-4460C>T

Variant summary

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

The ENST00000499522.6(BAALC-AS1):​n.71-4460C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,052 control chromosomes in the GnomAD database, including 1,978 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 0.15 (1978 hom., cov: 32)
• Consequence: BAALC-AS1 ENST00000499522.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369147	NR_148213.1	n.579+4675C>T		intron_variant	Intron 3 of 3
LOC105369147	NR_148214.1	n.531-4831C>T		intron_variant	Intron 2 of 3
LOC105369147	NR_148215.1	n.536-4831C>T		intron_variant	Intron 2 of 3
LOC105369147	NR_148216.1	n.470+25046C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAALC-AS1	ENST00000499522.6	n.71-4460C>T		intron_variant	Intron 1 of 5	5
BAALC-AS1	ENST00000519801.1	n.70+12535C>T		intron_variant	Intron 1 of 1	3
BAALC-AS1	ENST00000520025.1	n.69-4831C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23316 AN: 151934 Hom.: 1977 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.153 AC: 23321 AN: 152052 Hom.: 1978 Cov.: 32 AF XY: 0.157 AC XY: 11700 AN XY: 74314

African (AFR) AF: 0.116 AC: 4798 AN: 41496

American (AMR) AF: 0.184 AC: 2815 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1065 AN: 5180

South Asian (SAS) AF: 0.207 AC: 997 AN: 4810

European-Finnish (FIN) AF: 0.198 AC: 2083 AN: 10546

Middle Eastern (MID) AF: 0.199 AC: 57 AN: 286

European-Non Finnish (NFE) AF: 0.149 AC: 10109 AN: 67954

Other (OTH) AF: 0.162 AC: 342 AN: 2114

Alfa AF: 0.159 Hom.: 345

Bravo AF: 0.152

Asia WGS AF: 0.210 AC: 727 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	8.1
DANN	Benign	0.51
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs3107646; hg19: chr8-104285531;