rs4246823

chr5-178066866-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651496.2(FAM153CP):n.2446-149A>G variant causes a intron, non coding transcript 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 ENST00000651496.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM153CP	ENST00000651496.2	n.2446-149A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.708

Alfa AF: 0.706 Hom.: 63394

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4246823; hg19: chr5-177493867;