chr11-4541988-A-G

Variant names:

• chr11-4541988-A-G
• rs12416860

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 0.143 in 152,198 control chromosomes in the GnomAD database, including 1,795 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 0.14 (1795 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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: 0.143 AC: 21787 AN: 152080 Hom.: 1792 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0799

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0681

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.143 AC: 21820 AN: 152198 Hom.: 1795 Cov.: 33 AF XY: 0.138 AC XY: 10275 AN XY: 74418

African (AFR) AF: 0.229 AC: 9516 AN: 41518

American (AMR) AF: 0.0980 AC: 1498 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3468

East Asian (EAS) AF: 0.0797 AC: 413 AN: 5180

South Asian (SAS) AF: 0.103 AC: 498 AN: 4814

European-Finnish (FIN) AF: 0.0681 AC: 722 AN: 10604

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8069 AN: 68006

Other (OTH) AF: 0.148 AC: 313 AN: 2114

Alfa AF: 0.131 Hom.: 4886

Bravo AF: 0.150

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.7
DANN	Benign	0.44
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs12416860; hg19: chr11-4563218;