rs1502856

Variant names:

• chr1-50406175-G-A
• rs1502856
• ENST00000456841.2:n.-151C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-50406175-G-A
• chr1-50406175-G-C
• chr1-50406175-G-T

Variant summary

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

The ENST00000456841.2(FCF1P6):​n.-151C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,090 control chromosomes in the GnomAD database, including 20,987 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 0.51 (20987 hom., cov: 33)
• Consequence: FCF1P6 ENST00000456841.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 9 publications found

Genes affected

FCF1P6 (HGNC:44618): (FCF1 pseudogene 6)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456841.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCF1P6	ENST00000456841.2	TSL:6	n.-151C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77443 AN: 151972 Hom.: 20972 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.486

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.509 AC: 77470 AN: 152090 Hom.: 20987 Cov.: 33 AF XY: 0.522 AC XY: 38835 AN XY: 74358

African (AFR) AF: 0.354 AC: 14697 AN: 41468

American (AMR) AF: 0.604 AC: 9235 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1455 AN: 3470

East Asian (EAS) AF: 0.825 AC: 4276 AN: 5184

South Asian (SAS) AF: 0.643 AC: 3097 AN: 4818

European-Finnish (FIN) AF: 0.691 AC: 7306 AN: 10580

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35717 AN: 67962

Other (OTH) AF: 0.482 AC: 1017 AN: 2112

Alfa AF: 0.503 Hom.: 48377

Bravo AF: 0.495

Asia WGS AF: 0.666 AC: 2314 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.26
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs1502856; hg19: chr1-50871847;