rs549596

chr1-11856038-T-C

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 0.471 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.458

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.26
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

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