rs1554472

Variant names:

• chr4-156568754-G-A
• rs1554472

Your query was ambiguous. Multiple possible variants found:

• chr4-156568754-G-A
• chr4-156568754-G-C
• chr4-156568754-G-T

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 0.507 in 151,896 control chromosomes in the GnomAD database, including 19,787 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 0.51 (19787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.528 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: 0.507 AC: 76917 AN: 151780 Hom.: 19772 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.507 AC: 76976 AN: 151896 Hom.: 19787 Cov.: 32 AF XY: 0.502 AC XY: 37292 AN XY: 74234

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.546

Alfa AF: 0.487 Hom.: 5495

Bravo AF: 0.519

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554472; hg19: chr4-157489906;