rs3758096

Positions:

• chr8-103298265-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_148216.1(LOC105369147):​n.470+84A>C variant causes a intron, non coding transcript 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: 32)
• Consequence: LOC105369147 NR_148216.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

LOC105369147 (HGNC:):

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369147	NR_148216.1	n.470+84A>C		intron_variant, non_coding_transcript_variant
LOC105369147	NR_148213.1	n.470+84A>C		intron_variant, non_coding_transcript_variant
LOC105369147	NR_148214.1	n.470+84A>C		intron_variant, non_coding_transcript_variant
LOC105369147	NR_148215.1	n.470+84A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAALC-AS1	ENST00000521383.5	n.415+84A>C		intron_variant, non_coding_transcript_variant		3
BAALC-AS1	ENST00000522856.1	n.424+84A>C		intron_variant, non_coding_transcript_variant		3
BAALC-AS1	ENST00000523614.6	n.34+84A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758096; hg19: chr8-104310493;