rs4255548

chr11-69206503-A-Gchr11-69206503-A-T

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 0.628 in 150,090 control chromosomes in the GnomAD database, including 29,757 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 0.63 (29757 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 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: 0.628 AC: 94124 AN: 149974 Hom.: 29725 Cov.: 27

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.628 AC: 94209 AN: 150090 Hom.: 29757 Cov.: 27 AF XY: 0.630 AC XY: 46072 AN XY: 73188

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.642

Alfa AF: 0.620 Hom.: 43487

Bravo AF: 0.622

Asia WGS AF: 0.568 AC: 1916 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.9
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4255548; hg19: chr11-68973970;