rs1489572

Variant names:

• chr4-63169795-T-C
• rs1489572

Variant summary

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

The variant allele was found at a frequency of 0.504 in 151,852 control chromosomes in the GnomAD database, including 19,396 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 0.50 (19396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76481 AN: 151734 Hom.: 19365 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.504 AC: 76562 AN: 151852 Hom.: 19396 Cov.: 32 AF XY: 0.503 AC XY: 37308 AN XY: 74194

African (AFR) AF: 0.527 AC: 21834 AN: 41412

American (AMR) AF: 0.482 AC: 7339 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1838 AN: 3466

East Asian (EAS) AF: 0.380 AC: 1966 AN: 5168

South Asian (SAS) AF: 0.464 AC: 2238 AN: 4822

European-Finnish (FIN) AF: 0.511 AC: 5384 AN: 10538

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34308 AN: 67906

Other (OTH) AF: 0.504 AC: 1065 AN: 2114

Alfa AF: 0.514 Hom.: 2480

Bravo AF: 0.506

Asia WGS AF: 0.441 AC: 1527 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.47
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1489572; hg19: chr4-64035513;