14-76184421-T-C

Variant names:

• chr14-76184421-T-C
• rs2121070
• NM_017926.4:c.1193+3572T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017926.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPATCH2L	NM_017926.4	MANE Select	c.1193+3572T>C		intron	N/A	NP_060396.2
	GPATCH2L	NM_017972.3		c.1178+3572T>C		intron	N/A	NP_060442.2	Q9NWQ4-4
	GPATCH2L	NM_001322030.3		c.1193+3572T>C		intron	N/A	NP_001308959.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPATCH2L	ENST00000261530.12	TSL:2 MANE Select	c.1193+3572T>C		intron	N/A	ENSP00000261530.7	Q9NWQ4-3
	GPATCH2L	ENST00000930299.1		c.1193+3572T>C		intron	N/A	ENSP00000600358.1
	GPATCH2L	ENST00000954001.1		c.1193+3572T>C		intron	N/A	ENSP00000624060.1

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

African (AFR) AF: 0.600 AC: 24335 AN: 40572

American (AMR) AF: 0.839 AC: 12693 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2356 AN: 3464

East Asian (EAS) AF: 0.810 AC: 4093 AN: 5056

South Asian (SAS) AF: 0.877 AC: 4170 AN: 4754

European-Finnish (FIN) AF: 0.857 AC: 8952 AN: 10440

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.838 AC: 56877 AN: 67834

Other (OTH) AF: 0.751 AC: 1572 AN: 2092

Alfa AF: 0.802 Hom.: 93654

Bravo AF: 0.759

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.84
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2121070; hg19: chr14-76650764;