rs4551624

Variant names:

• chr1-200182696-T-C
• rs4551624

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 0.434 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.484 AC: 20067 AN: 41460

American (AMR) AF: 0.568 AC: 8682 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1455 AN: 3472

East Asian (EAS) AF: 0.771 AC: 3987 AN: 5168

South Asian (SAS) AF: 0.487 AC: 2347 AN: 4824

European-Finnish (FIN) AF: 0.317 AC: 3354 AN: 10568

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.363 AC: 24689 AN: 67972

Other (OTH) AF: 0.439 AC: 927 AN: 2114

Alfa AF: 0.405 Hom.: 23876

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4551624; hg19: chr1-200151824;