rs1047881

Positions:

• chr1-212857816-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027286.1(FLVCR1-DT):​n.323G>A 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 0.504 in 397,210 control chromosomes in the GnomAD database, including 52,509 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 0.46 (17521 hom., cov: 31)
  • Exomes 𝑓: 0.53 (34988 hom.)
• Consequence: FLVCR1-DT NR_027286.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLVCR1-DT	NR_027286.1	n.323G>A		non_coding_transcript_exon_variant	1/2
FLVCR1-DT	NR_027285.1	n.323G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLVCR1-DT	ENST00000356684.8	n.310G>A		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70311 AN: 151806 Hom.: 17522 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.465

GnomAD4 exome AF: 0.530 AC: 129920 AN: 245286 Hom.: 34988 Cov.: 0 AF XY: 0.531 AC XY: 66044 AN XY: 124380

Gnomad4 AFR exome AF: 0.290

Gnomad4 AMR exome AF: 0.354

Gnomad4 ASJ exome AF: 0.423

Gnomad4 EAS exome AF: 0.556

Gnomad4 SAS exome AF: 0.569

Gnomad4 FIN exome AF: 0.609

Gnomad4 NFE exome AF: 0.545

Gnomad4 OTH exome AF: 0.485

GnomAD4 genome AF: 0.463 AC: 70323 AN: 151924 Hom.: 17521 Cov.: 31 AF XY: 0.467 AC XY: 34641 AN XY: 74224

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.461

Alfa AF: 0.532 Hom.: 43996

Bravo AF: 0.432

Asia WGS AF: 0.506 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1047881; hg19: chr1-213031158; COSMIC: COSV63133939;