chr14-74446127-G-A

Position:

• chr14-74446127-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

SYNDIG1L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYNDIG1L	XM_017021600.2	c.-58+28177C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.533

Alfa AF: 0.507 Hom.: 25243

Bravo AF: 0.558

Asia WGS AF: 0.507 AC: 1752 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1125221; hg19: chr14-74912830;