rs1512288

Positions:

• chr4-144570129-G-A

Variant summary

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

The variant allele was found at a frequency of 0.414 in 152,036 control chromosomes in the GnomAD database, including 13,284 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 0.41 (13284 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62916 AN: 151918 Hom.: 13275 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.414 AC: 62963 AN: 152036 Hom.: 13284 Cov.: 33 AF XY: 0.419 AC XY: 31137 AN XY: 74298

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.378

Alfa AF: 0.429 Hom.: 7739

Bravo AF: 0.392

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1512288; hg19: chr4-145491281;