rs1047881

Variant names:

• chr1-212857816-C-G
• rs1047881
• ENST00000424044.4:n.323G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-212857816-C-G
• chr1-212857816-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000424044.4(FLVCR1-DT):​n.323G>C 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 0.00000407 in 245,490 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 31)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: FLVCR1-DT ENST00000424044.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 0 publications found

Genes affected

FLVCR1-DT (HGNC:39077): (FLVCR1 divergent transcript)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424044.4. 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
	FLVCR1-DT	NR_027285.1		n.323G>C		non_coding_transcript_exon	Exon 1 of 2
	FLVCR1-DT	NR_027286.1		n.323G>C		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FLVCR1-DT	ENST00000424044.4	TSL:1	n.323G>C		non_coding_transcript_exon	Exon 1 of 2
	FLVCR1-DT	ENST00000426161.9	TSL:1	n.494G>C		non_coding_transcript_exon	Exon 1 of 2
	FLVCR1-DT	ENST00000356684.9	TSL:2	n.342G>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000407 AC: 1 AN: 245490 Hom.: 0 Cov.: 0 AF XY: 0.00000803 AC XY: 1 AN XY: 124494

African (AFR) AF: 0.00 AC: 0 AN: 7172

American (AMR) AF: 0.00 AC: 0 AN: 7404

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9204

East Asian (EAS) AF: 0.0000438 AC: 1 AN: 22830

South Asian (SAS) AF: 0.00 AC: 0 AN: 2230

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21254

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1290

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 157714

Other (OTH) AF: 0.00 AC: 0 AN: 16392

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.45
PhyloP100		-0.63
PromoterAI		-0.16	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1047881; hg19: chr1-213031158;