rs1056189

Variant names:

• chr5-149634855-A-G
• rs1056189
• NM_001001669.3:c.*2664A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-149634855-A-G
• chr5-149634855-A-T

Variant summary

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

The NM_001001669.3(ARHGEF37):​c.*2664A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,532 control chromosomes in the GnomAD database, including 1,452 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 0.11 (1452 hom., cov: 32)
  • Exomes 𝑓: 0.014 (0 hom.)
• Consequence: ARHGEF37 NM_001001669.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 5 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGEF37	NM_001001669.3	c.*2664A>G		3_prime_UTR_variant	Exon 13 of 13	ENST00000333677.7	NP_001001669.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGEF37	ENST00000333677.7	c.*2664A>G		3_prime_UTR_variant	Exon 13 of 13	2	NM_001001669.3	ENSP00000328083.6

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16859 AN: 152066 Hom.: 1444 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0192

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.109

GnomAD4 exome AF: 0.0144 AC: 5 AN: 348 Hom.: 0 Cov.: 0 AF XY: 0.00962 AC XY: 2 AN XY: 208

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0146 AC: 5 AN: 342

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.111 AC: 16903 AN: 152184 Hom.: 1452 Cov.: 32 AF XY: 0.107 AC XY: 7978 AN XY: 74410

African (AFR) AF: 0.230 AC: 9531 AN: 41484

American (AMR) AF: 0.0977 AC: 1495 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3470

East Asian (EAS) AF: 0.170 AC: 878 AN: 5174

South Asian (SAS) AF: 0.102 AC: 493 AN: 4812

European-Finnish (FIN) AF: 0.0192 AC: 204 AN: 10612

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0535 AC: 3636 AN: 68020

Other (OTH) AF: 0.109 AC: 231 AN: 2110

Alfa AF: 0.0668 Hom.: 201

Bravo AF: 0.126

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.2
DANN	Benign	0.85
PhyloP100		-0.28
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: rs1056189; hg19: chr5-149014418;