rs1547888

Variant names:

• chr11-68149562-T-C
• rs1547888

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 0.223 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.228 AC: 9440 AN: 41470

American (AMR) AF: 0.166 AC: 2529 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1149 AN: 5170

South Asian (SAS) AF: 0.177 AC: 853 AN: 4818

European-Finnish (FIN) AF: 0.244 AC: 2584 AN: 10574

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15967 AN: 67984

Other (OTH) AF: 0.223 AC: 470 AN: 2104

Alfa AF: 0.216 Hom.: 1384

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
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1547888; hg19: chr11-67917029;