rs1551645

Variant names:

• chr4-55128147-T-G
• rs1551645

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 0.254 in 152,158 control chromosomes in the GnomAD database, including 5,315 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 0.25 (5315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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: 0.254 AC: 38617 AN: 152040 Hom.: 5317 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.254 AC: 38609 AN: 152158 Hom.: 5315 Cov.: 32 AF XY: 0.252 AC XY: 18750 AN XY: 74374

African (AFR) AF: 0.151 AC: 6275 AN: 41516

American (AMR) AF: 0.229 AC: 3501 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1359 AN: 3472

East Asian (EAS) AF: 0.178 AC: 923 AN: 5174

South Asian (SAS) AF: 0.258 AC: 1241 AN: 4818

European-Finnish (FIN) AF: 0.270 AC: 2854 AN: 10576

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21509 AN: 67996

Other (OTH) AF: 0.263 AC: 554 AN: 2108

Alfa AF: 0.263 Hom.: 840

Bravo AF: 0.246

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs1551645; hg19: chr4-55994314;