rs10270302

Positions:

• chr7-150515931-T-C

Variant summary

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

The NM_153236.4(GIMAP7):​c.-42+986T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,122 control chromosomes in the GnomAD database, including 2,911 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 0.19 (2911 hom., cov: 32)
• Consequence: GIMAP7 NM_153236.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

Genes affected

GIMAP7 (HGNC:22404): (GTPase, IMAP family member 7) This gene encodes a protein belonging to the GTP-binding superfamily and to the immuno-associated nucleotide (IAN) subfamily of nucleotide-binding proteins. In humans, the IAN subfamily genes are located in a cluster at 7q36.1. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP7	NM_153236.4	c.-42+986T>C		intron_variant		ENST00000313543.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP7	ENST00000313543.5	c.-42+986T>C		intron_variant		1	NM_153236.4	P1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28833 AN: 152002 Hom.: 2909 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.190 AC: 28863 AN: 152122 Hom.: 2911 Cov.: 32 AF XY: 0.184 AC XY: 13700 AN XY: 74376

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.190

Alfa AF: 0.201 Hom.: 4213

Bravo AF: 0.191

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.8
DANN	Benign	0.62

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: rs10270302; hg19: chr7-150213019;