rs3813546

Variant names:

• chr14-76153618-A-G
• rs3813546
• NM_017926.4:c.-10-736A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017926.4(GPATCH2L):​c.-10-736A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,198 control chromosomes in the GnomAD database, including 2,514 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 0.18 (2514 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: GPATCH2L NM_017926.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPATCH2L	NM_017926.4	c.-10-736A>G		intron_variant	Intron 1 of 9	ENST00000261530.12	NP_060396.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPATCH2L	ENST00000261530.12	c.-10-736A>G		intron_variant	Intron 1 of 9	2	NM_017926.4	ENSP00000261530.7

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27030 AN: 152080 Hom.: 2514 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.214

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.178 AC: 27043 AN: 152198 Hom.: 2514 Cov.: 33 AF XY: 0.177 AC XY: 13203 AN XY: 74428

African (AFR) AF: 0.153 AC: 6368 AN: 41512

American (AMR) AF: 0.155 AC: 2377 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3470

East Asian (EAS) AF: 0.190 AC: 988 AN: 5188

South Asian (SAS) AF: 0.126 AC: 609 AN: 4822

European-Finnish (FIN) AF: 0.178 AC: 1885 AN: 10606

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12937 AN: 67990

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.189 Hom.: 3588

Bravo AF: 0.175

Asia WGS AF: 0.149 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.59
PhyloP100		-0.31
PromoterAI		-0.013	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3813546; hg19: chr14-76619961;