rs4551624

Variant names:

• chr1-200182696-T-C
• rs4551624

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 0.434 in 152,056 control chromosomes in the GnomAD database, including 15,185 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 0.43 (15185 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 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: 0.434 AC: 65962 AN: 151938 Hom.: 15165 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.434 AC: 66020 AN: 152056 Hom.: 15185 Cov.: 32 AF XY: 0.437 AC XY: 32485 AN XY: 74328

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.439

Alfa AF: 0.395 Hom.: 15100

Bravo AF: 0.461

Asia WGS AF: 0.593 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4551624; hg19: chr1-200151824;