rs1379544

Variant names:

• chr5-149601483-T-C
• rs1379544
• NM_001001669.3:c.310+252T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001669.3(ARHGEF37):​c.310+252T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,038 control chromosomes in the GnomAD database, including 23,502 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 0.55 (23502 hom., cov: 32)
• Consequence: ARHGEF37 NM_001001669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGEF37	NM_001001669.3	c.310+252T>C		intron_variant	Intron 3 of 12	ENST00000333677.7	NP_001001669.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGEF37	ENST00000333677.7	c.310+252T>C		intron_variant	Intron 3 of 12	2	NM_001001669.3	ENSP00000328083.6

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83747 AN: 151920 Hom.: 23461 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.551 AC: 83845 AN: 152038 Hom.: 23502 Cov.: 32 AF XY: 0.554 AC XY: 41151 AN XY: 74302

African (AFR) AF: 0.561 AC: 23274 AN: 41460

American (AMR) AF: 0.649 AC: 9923 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.714 AC: 3692 AN: 5168

South Asian (SAS) AF: 0.683 AC: 3283 AN: 4806

European-Finnish (FIN) AF: 0.439 AC: 4647 AN: 10578

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.521 AC: 35433 AN: 67966

Other (OTH) AF: 0.552 AC: 1163 AN: 2106

Alfa AF: 0.539 Hom.: 89680

Bravo AF: 0.569

Asia WGS AF: 0.734 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.2
DANN	Benign	0.57
PhyloP100		0.17
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: rs1379544; hg19: chr5-148981046;