rs1554690

Variant names:

• chr7-146049240-A-C
• rs1554690

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 0.423 in 151,782 control chromosomes in the GnomAD database, including 13,912 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 0.42 (13912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 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: 0.423 AC: 64172 AN: 151664 Hom.: 13882 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.423 AC: 64244 AN: 151782 Hom.: 13912 Cov.: 32 AF XY: 0.420 AC XY: 31134 AN XY: 74170

African (AFR) AF: 0.506 AC: 20956 AN: 41444

American (AMR) AF: 0.294 AC: 4479 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2302 AN: 5166

South Asian (SAS) AF: 0.482 AC: 2323 AN: 4820

European-Finnish (FIN) AF: 0.360 AC: 3804 AN: 10552

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27598 AN: 67804

Other (OTH) AF: 0.417 AC: 879 AN: 2108

Alfa AF: 0.408 Hom.: 18296

Bravo AF: 0.416

Asia WGS AF: 0.471 AC: 1634 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.58
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1554690; hg19: chr7-145746333;