rs7156960

Variant names:

• chr14-76237008-C-G
• rs7156960
• ENST00000554225.1:n.187+1005C>G

Your query was ambiguous. Multiple possible variants found:

• chr14-76237008-C-G
• chr14-76237008-C-T

Variant summary

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

The ENST00000556372.2(GPATCH2L):​n.*117+7055C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,902 control chromosomes in the GnomAD database, including 14,639 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 0.44 (14639 hom., cov: 32)
• Consequence: GPATCH2L ENST00000556372.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944

Genes affected

ENSG00000258454 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370575	XR_001750833.3	n.663-8358G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258454	ENST00000554225.1	n.187+1005C>G		intron_variant	Intron 1 of 2	3
GPATCH2L	ENST00000556372.2	n.*117+7055C>G		intron_variant	Intron 2 of 3	3		ENSP00000451827.2

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66154 AN: 151784 Hom.: 14633 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.436 AC: 66193 AN: 151902 Hom.: 14639 Cov.: 32 AF XY: 0.437 AC XY: 32468 AN XY: 74218

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.424

Alfa AF: 0.428 Hom.: 7460

Bravo AF: 0.432

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7156960; hg19: chr14-76703351;