7-150520160-A-G

Variant names:

• chr7-150520160-A-G
• rs3735081
• NM_153236.4:c.186A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_153236.4(GIMAP7):​c.186A>G​(p.Val62Val) 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
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GIMAP7	NM_153236.4	c.186A>G	p.Val62Val	synonymous_variant	Exon 2 of 2	ENST00000313543.5	NP_694968.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP7	ENST00000313543.5	c.186A>G	p.Val62Val	synonymous_variant	Exon 2 of 2	1	NM_153236.4	ENSP00000315474.4

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

GnomAD2 exomes AF: 0.690 AC: 173408 AN: 251216 AF XY: 0.687

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 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

African (AFR) AF: 0.934 AC: 31286 AN: 33480

American (AMR) AF: 0.699 AC: 31233 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 17366 AN: 26134

East Asian (EAS) AF: 0.735 AC: 29185 AN: 39700

South Asian (SAS) AF: 0.743 AC: 64063 AN: 86258

European-Finnish (FIN) AF: 0.738 AC: 39434 AN: 53406

Middle Eastern (MID) AF: 0.639 AC: 3686 AN: 5768

European-Non Finnish (NFE) AF: 0.623 AC: 692394 AN: 1111930

Other (OTH) AF: 0.667 AC: 40296 AN: 60394

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

African (AFR) AF: 0.923 AC: 38324 AN: 41508

American (AMR) AF: 0.698 AC: 10657 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2338 AN: 3472

East Asian (EAS) AF: 0.730 AC: 3773 AN: 5168

South Asian (SAS) AF: 0.755 AC: 3639 AN: 4818

European-Finnish (FIN) AF: 0.764 AC: 8055 AN: 10550

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42799 AN: 67956

Other (OTH) AF: 0.689 AC: 1453 AN: 2108

Alfa AF: 0.660 Hom.: 160482

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
PhyloP100		-3.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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