rs4341514

Variant names:

• chr11-2120373-A-G
• rs4341514

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 0.52 in 152,152 control chromosomes in the GnomAD database, including 22,701 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 0.52 (22701 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• Publications: 14 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 (AMR) allele frequency at 95% confidence interval = 0.636 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: 0.521 AC: 79137 AN: 152034 Hom.: 22687 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.520 AC: 79180 AN: 152152 Hom.: 22701 Cov.: 33 AF XY: 0.523 AC XY: 38890 AN XY: 74374

African (AFR) AF: 0.263 AC: 10918 AN: 41526

American (AMR) AF: 0.647 AC: 9884 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2077 AN: 3470

East Asian (EAS) AF: 0.486 AC: 2503 AN: 5154

South Asian (SAS) AF: 0.468 AC: 2256 AN: 4824

European-Finnish (FIN) AF: 0.653 AC: 6916 AN: 10586

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42665 AN: 67988

Other (OTH) AF: 0.523 AC: 1106 AN: 2114

Alfa AF: 0.564 Hom.: 46636

Bravo AF: 0.509

Asia WGS AF: 0.489 AC: 1702 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	0.19
DANN	Benign	0.21
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs4341514; hg19: chr11-2141603;