rs1125221

Variant names:

• chr14-74446127-G-A
• rs1125221
• XM_017021600.2:c.-58+28177C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-74446127-G-A
• chr14-74446127-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017021600.2(SYNDIG1L):​c.-58+28177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,990 control chromosomes in the GnomAD database, including 23,883 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 0.55 (23883 hom., cov: 32)
• Consequence: SYNDIG1L XM_017021600.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 9 publications found

Genes affected

SYNDIG1L (HGNC:32388): (synapse differentiation inducing 1 like) Predicted to be located in Golgi apparatus. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle and membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84033 AN: 151870 Hom.: 23865 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.553 AC: 84098 AN: 151990 Hom.: 23883 Cov.: 32 AF XY: 0.552 AC XY: 41023 AN XY: 74272

African (AFR) AF: 0.686 AC: 28440 AN: 41470

American (AMR) AF: 0.518 AC: 7909 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2050 AN: 3466

East Asian (EAS) AF: 0.352 AC: 1824 AN: 5176

South Asian (SAS) AF: 0.608 AC: 2932 AN: 4824

European-Finnish (FIN) AF: 0.488 AC: 5143 AN: 10538

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.501 AC: 34023 AN: 67954

Other (OTH) AF: 0.533 AC: 1124 AN: 2108

Alfa AF: 0.509 Hom.: 30589

Bravo AF: 0.558

Asia WGS AF: 0.507 AC: 1752 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.55
DANN	Benign	0.84
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1125221; hg19: chr14-74912830;