rs4246823

Variant names:

• chr5-178066866-A-G
• rs4246823
• ENST00000651483.1:n.1506A>G

Variant summary

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

The ENST00000651483.1(FAM153CP):​n.1506A>G 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 0.712 in 150,914 control chromosomes in the GnomAD database, including 38,413 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 0.71 (38413 hom., cov: 27)
• Consequence: FAM153CP ENST00000651483.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 4 publications found

Genes affected

FAM153CP (HGNC:33936): (family with sequence similarity 153 member C, pseudogene)

ENSG00000309599 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM153CP	ENST00000651483.1	n.1506A>G		non_coding_transcript_exon_variant	Exon 1 of 1
FAM153CP	ENST00000651413.2	n.5726+12059A>G		intron_variant	Intron 14 of 14
FAM153CP	ENST00000651496.3	n.*1146-149A>G		intron_variant	Intron 14 of 15			ENSP00000520387.1

Frequencies

GnomAD3 genomes AF: 0.713 AC: 107452 AN: 150808 Hom.: 38386 Cov.: 27

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.712 AC: 107524 AN: 150914 Hom.: 38413 Cov.: 27 AF XY: 0.716 AC XY: 52699 AN XY: 73570

African (AFR) AF: 0.712 AC: 29188 AN: 41016

American (AMR) AF: 0.686 AC: 10369 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2573 AN: 3470

East Asian (EAS) AF: 0.885 AC: 4523 AN: 5112

South Asian (SAS) AF: 0.719 AC: 3442 AN: 4784

European-Finnish (FIN) AF: 0.729 AC: 7451 AN: 10222

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47532 AN: 67884

Other (OTH) AF: 0.708 AC: 1486 AN: 2098

Alfa AF: 0.705 Hom.: 141215

Bravo AF: 0.711

Asia WGS AF: 0.780 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4246823; hg19: chr5-177493867;