chr4-175937875-A-T

Position:

• chr4-175937875-A-T

Variant summary

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

The ENST00000280187.11(GPM6A):​c.-23+64434T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,892 control chromosomes in the GnomAD database, including 3,153 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 0.15 (3153 hom., cov: 32)
• Consequence: GPM6A ENST00000280187.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984113	XR_001741924.3	n.490+9770T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPM6A	ENST00000280187.11	c.-23+64434T>A		intron_variant		1		ENSP00000280187	P1
GPM6A	ENST00000506894.5	c.4+64434T>A		intron_variant		1		ENSP00000421578
GPM6A	ENST00000502754.5	c.-153+34002T>A		intron_variant		2		ENSP00000426821

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22939 AN: 151776 Hom.: 3147 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0504

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0508

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.151 AC: 22974 AN: 151892 Hom.: 3153 Cov.: 32 AF XY: 0.150 AC XY: 11172 AN XY: 74264

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.0908

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0504

Gnomad4 NFE AF: 0.0508

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0739 Hom.: 443

Bravo AF: 0.160

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.41

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: rs7687921; hg19: chr4-176859026;