rs1547888

Positions:

• chr11-68149562-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 0.223 in 152,074 control chromosomes in the GnomAD database, including 3,840 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 0.22 (3840 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68149562T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33951 AN: 151956 Hom.: 3842 Cov.: 30

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.223 AC: 33962 AN: 152074 Hom.: 3840 Cov.: 30 AF XY: 0.222 AC XY: 16491 AN XY: 74346

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.223

Alfa AF: 0.220 Hom.: 786

Bravo AF: 0.218

Asia WGS AF: 0.209 AC: 725 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	0.64
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547888; hg19: chr11-67917029;