rs1489572

Positions:

• chr4-63169795-T-C

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 0.504 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.504

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1489572; hg19: chr4-64035513;