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. The variant received -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
• Publications: 13 publications found

Genes affected

ENSG00000258454 (HGNC:):

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556372.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258454	ENST00000554225.1	TSL:3	n.187+1005C>G		intron	N/A
	GPATCH2L	ENST00000556372.2	TSL:3	n.*117+7055C>G		intron	N/A	ENSP00000451827.2	G3V4I8
	ENSG00000258402	ENST00000720628.1		n.451-8358G>C		intron	N/A

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

African (AFR) AF: 0.370 AC: 15312 AN: 41414

American (AMR) AF: 0.452 AC: 6914 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1484 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2757 AN: 5136

South Asian (SAS) AF: 0.466 AC: 2239 AN: 4808

European-Finnish (FIN) AF: 0.483 AC: 5095 AN: 10544

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30773 AN: 67932

Other (OTH) AF: 0.424 AC: 894 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.50
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs7156960; hg19: chr14-76703351;