rs12719740

Variant names:

• chr15-98529676-G-A
• rs12719740
• ENST00000637259.1:n.575-9287C>T

Variant summary

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

The ENST00000637259.1(FAM169BP):​n.575-9287C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,014 control chromosomes in the GnomAD database, including 3,386 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 0.21 (3386 hom., cov: 32)
• Consequence: FAM169BP ENST00000637259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649

Genes affected

FAM169BP (HGNC:26835): (family with sequence similarity 169 member B, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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
FAM169BP	ENST00000637259.1	n.575-9287C>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31580 AN: 151896 Hom.: 3383 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.208 AC: 31597 AN: 152014 Hom.: 3386 Cov.: 32 AF XY: 0.211 AC XY: 15663 AN XY: 74298

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.184

Alfa AF: 0.184 Hom.: 5599

Bravo AF: 0.211

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.38
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12719740; hg19: chr15-99072905;