rs2121070

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr14-76184421-T-A
• chr14-76184421-T-C
• chr14-76184421-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017926.4(GPATCH2L):​c.1193+3572T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).

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>A		intron	N/A	NP_060396.2
	GPATCH2L	NM_017972.3		c.1178+3572T>A		intron	N/A	NP_060442.2	Q9NWQ4-4
	GPATCH2L	NM_001322030.3		c.1193+3572T>A		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>A		intron	N/A	ENSP00000261530.7	Q9NWQ4-3
	GPATCH2L	ENST00000930299.1		c.1193+3572T>A		intron	N/A	ENSP00000600358.1
	GPATCH2L	ENST00000954001.1		c.1193+3572T>A		intron	N/A	ENSP00000624060.1

Frequencies

GnomAD3 genomes Cov.: 25

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

GnomAD4 genome Cov.: 25

Alfa AF: 0.00 Hom.: 93654

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.7
DANN	Benign	0.82
PhyloP100		-0.60

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;