rs41341649

Positions:

• chr1-229260325-C-G
• chr1-229260325-C-A

Variant summary

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

The NR_149313.1(RAB4A-AS1):​n.180-1205G>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: 29)
• Consequence: RAB4A-AS1 NR_149313.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

RAB4A-AS1 (HGNC:55934): (RAB4A 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=-1.07).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB4A-AS1	NR_149313.1	n.180-1205G>C		intron_variant, non_coding_transcript_variant
RAB4A-AS1	NR_149312.1	n.1854-1205G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB4A-AS1	ENST00000654028.1	n.171-1205G>C		intron_variant, non_coding_transcript_variant
RAB4A-AS1	ENST00000429227.1	n.29-1205G>C		intron_variant, non_coding_transcript_variant		5
RAB4A-AS1	ENST00000653511.1	n.1740-1205G>C		intron_variant, non_coding_transcript_variant
RAB4A-AS1	ENST00000656366.1	n.1447-1205G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.087

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-229396072;