rs4690647

chr4-175951769-G-Achr4-175951769-G-Cchr4-175951769-G-T

Variant summary

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

The ENST00000280187.11(GPM6A):c.-23+50540C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,078 control chromosomes in the GnomAD database, including 22,934 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 0.52 (22934 hom., cov: 33)
• Consequence: GPM6A ENST00000280187.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

Genes affected

GPM6A (HGNC:4460): (glycoprotein M6A) Predicted to enable calcium channel activity. Involved in neuron migration and stem cell differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

LOC107984113 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984113	XR_001741924.3	n.437-4071C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPM6A	ENST00000280187.11	c.-23+50540C>T		intron_variant		1		P1
GPM6A	ENST00000506894.5	c.4+50540C>T		intron_variant		1
GPM6A	ENST00000502754.5	c.-153+20108C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78470 AN: 151960 Hom.: 22931 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.516 AC: 78484 AN: 152078 Hom.: 22934 Cov.: 33 AF XY: 0.518 AC XY: 38535 AN XY: 74332

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.542

Alfa AF: 0.611 Hom.: 51415

Bravo AF: 0.507

Asia WGS AF: 0.445 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.78
Dann	Benign	0.45

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

Publications

LitVar

Other links and lift over

dbSNP: rs4690647; hg19: chr4-176872920;