5-178073953-G-C

Variant names:

• chr5-178073953-G-C
• rs11745917
• ENST00000651413.2:n.5727-12291G>C

Variant summary

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

The ENST00000651413.2(FAM153CP):​n.5727-12291G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,726 control chromosomes in the GnomAD database, including 3,878 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 0.22 (3878 hom., cov: 32)
• Consequence: FAM153CP ENST00000651413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651413.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM153CP	ENST00000651413.2		n.5727-12291G>C		intron	N/A
	ENSG00000309599	ENST00000842241.1		n.463+2070C>G		intron	N/A
	ENSG00000309599	ENST00000842242.1		n.568+2070C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33605 AN: 151608 Hom.: 3875 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.222 AC: 33624 AN: 151726 Hom.: 3878 Cov.: 32 AF XY: 0.218 AC XY: 16164 AN XY: 74134

African (AFR) AF: 0.177 AC: 7342 AN: 41368

American (AMR) AF: 0.243 AC: 3702 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3466

East Asian (EAS) AF: 0.102 AC: 523 AN: 5118

South Asian (SAS) AF: 0.250 AC: 1203 AN: 4810

European-Finnish (FIN) AF: 0.222 AC: 2346 AN: 10554

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17260 AN: 67870

Other (OTH) AF: 0.223 AC: 470 AN: 2112

Alfa AF: 0.245 Hom.: 577

Bravo AF: 0.218

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.68
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs11745917; hg19: chr5-177500954;