rs11225547

Variant names:

• chr11-103097123-A-C
• rs11225547

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 0.045 in 152,262 control chromosomes in the GnomAD database, including 215 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 0.045 (215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0621 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: 0.0450 AC: 6850 AN: 152144 Hom.: 214 Cov.: 32

Gnomad AFR AF: 0.0127

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.00789

Gnomad SAS AF: 0.0572

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0450 AC: 6852 AN: 152262 Hom.: 215 Cov.: 32 AF XY: 0.0446 AC XY: 3323 AN XY: 74462

African (AFR) AF: 0.0127 AC: 527 AN: 41550

American (AMR) AF: 0.0565 AC: 864 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0648 AC: 225 AN: 3472

East Asian (EAS) AF: 0.00791 AC: 41 AN: 5186

South Asian (SAS) AF: 0.0581 AC: 280 AN: 4822

European-Finnish (FIN) AF: 0.0211 AC: 224 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0637 AC: 4332 AN: 68000

Other (OTH) AF: 0.0639 AC: 135 AN: 2112

Alfa AF: 0.0608 Hom.: 165

Bravo AF: 0.0469

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.74
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs11225547; hg19: chr11-102967852;