rs1514823

Variant names:

• chr11-41919956-T-A
• rs1514823

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 0.251 in 152,048 control chromosomes in the GnomAD database, including 8,192 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 0.25 (8192 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 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: 0.251 AC: 38076 AN: 151930 Hom.: 8172 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.251 AC: 38141 AN: 152048 Hom.: 8192 Cov.: 32 AF XY: 0.247 AC XY: 18381 AN XY: 74330

African (AFR) AF: 0.584 AC: 24197 AN: 41408

American (AMR) AF: 0.138 AC: 2102 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1133 AN: 5164

South Asian (SAS) AF: 0.206 AC: 993 AN: 4820

European-Finnish (FIN) AF: 0.0991 AC: 1050 AN: 10598

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7791 AN: 68000

Other (OTH) AF: 0.203 AC: 427 AN: 2108

Alfa AF: 0.191 Hom.: 640

Bravo AF: 0.268

Asia WGS AF: 0.227 AC: 787 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	0.47
DANN	Benign	0.31
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1514823; hg19: chr11-41941506;