7-150520160-A-G

Position:

• chr7-150520160-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_153236.4(GIMAP7):​c.186A>G​(p.Val62=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 1,613,844 control chromosomes in the GnomAD database, including 353,099 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 0.74 (42384 hom., cov: 31)
  • Exomes 𝑓: 0.65 (310715 hom.)
• Consequence: GIMAP7 NM_153236.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.63

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP7: Synonymous conserved (PhyloP=-3.63 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP7	NM_153236.4	c.186A>G	p.Val62=	synonymous_variant	2/2	ENST00000313543.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP7	ENST00000313543.5	c.186A>G	p.Val62=	synonymous_variant	2/2	1	NM_153236.4	P1

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111775 AN: 151944 Hom.: 42325 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.686

GnomAD3 exomes AF: 0.690 AC: 173408 AN: 251216 Hom.: 60653 AF XY: 0.687 AC XY: 93241 AN XY: 135774

Gnomad AFR exome AF: 0.933

Gnomad AMR exome AF: 0.698

Gnomad ASJ exome AF: 0.664

Gnomad EAS exome AF: 0.711

Gnomad SAS exome AF: 0.743

Gnomad FIN exome AF: 0.746

Gnomad NFE exome AF: 0.629

Gnomad OTH exome AF: 0.661

GnomAD4 exome AF: 0.649 AC: 948943 AN: 1461782 Hom.: 310715 Cov.: 61 AF XY: 0.651 AC XY: 473416 AN XY: 727192

Gnomad4 AFR exome AF: 0.934

Gnomad4 AMR exome AF: 0.699

Gnomad4 ASJ exome AF: 0.664

Gnomad4 EAS exome AF: 0.735

Gnomad4 SAS exome AF: 0.743

Gnomad4 FIN exome AF: 0.738

Gnomad4 NFE exome AF: 0.623

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.736 AC: 111891 AN: 152062 Hom.: 42384 Cov.: 31 AF XY: 0.740 AC XY: 55028 AN XY: 74322

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.689

Alfa AF: 0.648 Hom.: 76023

Bravo AF: 0.737

Asia WGS AF: 0.771 AC: 2684 AN: 3478

EpiCase AF: 0.624

EpiControl AF: 0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.59

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: rs3735081; hg19: chr7-150217248; COSMIC: COSV57959382;