1-212857816-C-T

Variant names:

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

Variant summary

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

The ENST00000424044.4(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 ENST00000424044.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 26 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FLVCR1-DT	NR_027285.1	n.323G>A		non_coding_transcript_exon_variant	Exon 1 of 2
FLVCR1-DT	NR_027286.1	n.323G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLVCR1-DT	ENST00000424044.4	n.323G>A		non_coding_transcript_exon_variant	Exon 1 of 2	1
FLVCR1-DT	ENST00000426161.9	n.494G>A		non_coding_transcript_exon_variant	Exon 1 of 2	1
FLVCR1-DT	ENST00000356684.9	n.342G>A		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR) AF: 0.290 AC: 2078 AN: 7170

American (AMR) AF: 0.354 AC: 2618 AN: 7400

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 3890 AN: 9196

East Asian (EAS) AF: 0.556 AC: 12697 AN: 22816

South Asian (SAS) AF: 0.569 AC: 1267 AN: 2228

European-Finnish (FIN) AF: 0.609 AC: 12941 AN: 21240

Middle Eastern (MID) AF: 0.484 AC: 622 AN: 1286

European-Non Finnish (NFE) AF: 0.545 AC: 85864 AN: 157570

Other (OTH) AF: 0.485 AC: 7943 AN: 16380

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

African (AFR) AF: 0.289 AC: 11972 AN: 41450

American (AMR) AF: 0.372 AC: 5681 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2807 AN: 5136

South Asian (SAS) AF: 0.542 AC: 2610 AN: 4812

European-Finnish (FIN) AF: 0.622 AC: 6566 AN: 10562

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37714 AN: 67920

Other (OTH) AF: 0.461 AC: 974 AN: 2112

Alfa AF: 0.514 Hom.: 64207

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
PhyloP100		-0.63
PromoterAI		-0.021	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; COSMIC: COSV63133939;