dbSNP rs1047881: FLVCR1-DT:n.323G>C (chr1-212857816-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.627

Publications

0 publications found

Variant links:

Genes affected

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

FLVCR1-DT links:

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ACMG classification

Classification was made for transcript

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLVCR1-DT	NR_027285.1 link	n.323G>C		non_coding_transcript_exon_variant	Exon 1 of 2
FLVCR1-DT	NR_027286.1 link	n.323G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
FLVCR1-DT	ENST00000424044.4 link	n.323G>C	non_coding_transcript_exon_variant	Exon 1 of 2	1
FLVCR1-DT	ENST00000426161.9 link	n.494G>C	non_coding_transcript_exon_variant	Exon 1 of 2	1
FLVCR1-DT	ENST00000356684.9 link	n.342G>C	non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000407

AC:

AN:

245490

Hom.:

Cov.:

AF XY:

0.00000803

AC XY:

AN XY:

124494

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

7172

American (AMR)

AF:

0.00

AC:

AN:

7404

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9204

East Asian (EAS)

AF:

0.0000438

AC:

AN:

22830

South Asian (SAS)

AF:

0.00

AC:

AN:

2230

European-Finnish (FIN)

AF:

0.00

AC:

AN:

21254

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1290

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

157714

Other (OTH)

AF:

0.00

AC:

AN:

16392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.6

(source)

DANN

Benign

0.45

PhyloP100

-0.63

PromoterAI

-0.16

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over