rs549596

Variant names:

• chr1-11856038-T-C
• rs549596

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 0.471 in 151,188 control chromosomes in the GnomAD database, including 17,771 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 0.47 (17771 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71058 AN: 151064 Hom.: 17737 Cov.: 30

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.471 AC: 71141 AN: 151188 Hom.: 17771 Cov.: 30 AF XY: 0.465 AC XY: 34345 AN XY: 73820

African (AFR) AF: 0.637 AC: 26253 AN: 41238

American (AMR) AF: 0.323 AC: 4870 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1466 AN: 3466

East Asian (EAS) AF: 0.206 AC: 1046 AN: 5088

South Asian (SAS) AF: 0.532 AC: 2550 AN: 4790

European-Finnish (FIN) AF: 0.380 AC: 3972 AN: 10444

Middle Eastern (MID) AF: 0.517 AC: 150 AN: 290

European-Non Finnish (NFE) AF: 0.435 AC: 29513 AN: 67796

Other (OTH) AF: 0.458 AC: 962 AN: 2100

Alfa AF: 0.453 Hom.: 2043

Bravo AF: 0.468

Asia WGS AF: 0.397 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.23
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs549596; hg19: chr1-11916095; COSMIC: COSV64687418;