rs7715047

Positions:

• chr5-149606228-C-T

Variant summary

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

The NM_001001669.3(ARHGEF37):​c.311-3320C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,048 control chromosomes in the GnomAD database, including 10,761 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 0.34 (10761 hom., cov: 32)
• Consequence: ARHGEF37 NM_001001669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628

Genes affected

ARHGEF37 (HGNC:34430): (Rho guanine nucleotide exchange factor 37) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of catalytic activity. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGEF37	NM_001001669.3	c.311-3320C>T		intron_variant		ENST00000333677.7	NP_001001669.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGEF37	ENST00000333677.7	c.311-3320C>T		intron_variant		2	NM_001001669.3	ENSP00000328083	P1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51351 AN: 151930 Hom.: 10766 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.338 AC: 51341 AN: 152048 Hom.: 10761 Cov.: 32 AF XY: 0.335 AC XY: 24927 AN XY: 74306

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.364

Alfa AF: 0.438 Hom.: 14425

Bravo AF: 0.309

Asia WGS AF: 0.129 AC: 452 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	1.4
DANN	Benign	0.78

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: rs7715047; hg19: chr5-148985791;