chr4-175916638-C-A

Position:

• chr4-175916638-C-A

Variant summary

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

The ENST00000280187.11(GPM6A):​c.-23+85671G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,048 control chromosomes in the GnomAD database, including 27,040 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 0.55 (27040 hom., cov: 31)
• Consequence: GPM6A ENST00000280187.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984113	XR_001741924.3	n.491-7974G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPM6A	ENST00000280187.11	c.-23+85671G>T		intron_variant		1		P1
GPM6A	ENST00000506894.5	c.4+85671G>T		intron_variant		1
GPM6A	ENST00000502754.5	c.-153+55239G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83530 AN: 151932 Hom.: 27042 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.549 AC: 83524 AN: 152048 Hom.: 27040 Cov.: 31 AF XY: 0.550 AC XY: 40830 AN XY: 74294

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.583

Alfa AF: 0.673 Hom.: 46970

Bravo AF: 0.538

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.64

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: rs1495714; hg19: chr4-176837789;