1-212864319-G-T

Position:

• chr1-212864319-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000366971.9(FLVCR1):​c.883+450G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 258,102 control chromosomes in the GnomAD database, including 29,108 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 0.44 (15686 hom., cov: 33)
  • Exomes 𝑓: 0.49 (13422 hom.)
• Consequence: FLVCR1 ENST00000366971.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.802

Genes affected

FLVCR1 (HGNC:24682): (FLVCR choline and heme transporter 1) This gene encodes a member of the major facilitator superfamily of transporter proteins. The encoded protein is a heme transporter that may play a critical role in erythropoiesis by protecting developing erythroid cells from heme toxicity. This gene may play a role in posterior column ataxia with retinitis pigmentosa and the hematological disorder Diamond-Blackfan syndrome. [provided by RefSeq, Jan 2011]

FLVCR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLVCR1	NM_014053.4	c.883+450G>T		intron_variant		ENST00000366971.9	NP_054772.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLVCR1	ENST00000366971.9	c.883+450G>T		intron_variant		1	NM_014053.4	ENSP00000355938.4
FLVCR1	ENST00000419102.1	c.418+450G>T		intron_variant		5		ENSP00000414680.1
FLVCR1	ENST00000579295.1	n.240-74G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66713 AN: 151894 Hom.: 15689 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.434

GnomAD4 exome AF: 0.493 AC: 52329 AN: 106090 Hom.: 13422 AF XY: 0.488 AC XY: 27639 AN XY: 56604

Gnomad4 AFR exome AF: 0.276

Gnomad4 AMR exome AF: 0.339

Gnomad4 ASJ exome AF: 0.389

Gnomad4 EAS exome AF: 0.501

Gnomad4 SAS exome AF: 0.458

Gnomad4 FIN exome AF: 0.601

Gnomad4 NFE exome AF: 0.518

Gnomad4 OTH exome AF: 0.490

GnomAD4 genome AF: 0.439 AC: 66724 AN: 152012 Hom.: 15686 Cov.: 33 AF XY: 0.444 AC XY: 32956 AN XY: 74308

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.431

Alfa AF: 0.464 Hom.: 4030

Bravo AF: 0.409

Asia WGS AF: 0.476 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	21
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs963328; hg19: chr1-213037661;