14-76184421-T-C

Position:

• chr14-76184421-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017926.4(GPATCH2L):​c.1193+3572T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 150,534 control chromosomes in the GnomAD database, including 45,546 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 0.77 (45546 hom., cov: 25)
• Consequence: GPATCH2L NM_017926.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

Genes affected

GPATCH2L (HGNC:20210): (G-patch domain containing 2 like)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPATCH2L	NM_017926.4	c.1193+3572T>C		intron_variant		ENST00000261530.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPATCH2L	ENST00000261530.12	c.1193+3572T>C		intron_variant		2	NM_017926.4	A1

Frequencies

GnomAD3 genomes AF: 0.771 AC: 115942 AN: 150418 Hom.: 45519 Cov.: 25

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.771 AC: 116024 AN: 150534 Hom.: 45546 Cov.: 25 AF XY: 0.774 AC XY: 56921 AN XY: 73530

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.751

Alfa AF: 0.817 Hom.: 56535

Bravo AF: 0.759

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2121070; hg19: chr14-76650764;