rs950943

Variant names:

• chr3-154034437-A-T
• rs950943
• ENST00000491862.6:n.358-4061T>A

Variant summary

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

The ENST00000491862.6(ARHGEF26-AS1):​n.358-4061T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,080 control chromosomes in the GnomAD database, including 10,533 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 0.36 (10533 hom., cov: 32)
• Consequence: ARHGEF26-AS1 ENST00000491862.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 0 publications found

Genes affected

ARHGEF26-AS1 (HGNC:41048): (ARHGEF26 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000491862.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGEF26-AS1	NR_037901.1		n.257-4061T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGEF26-AS1	ENST00000491862.6	TSL:1	n.358-4061T>A		intron	N/A
	ARHGEF26-AS1	ENST00000467912.6	TSL:3	n.360-4058T>A		intron	N/A
	ARHGEF26-AS1	ENST00000479270.6	TSL:4	n.379-4058T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53971 AN: 151962 Hom.: 10530 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.355 AC: 54001 AN: 152080 Hom.: 10533 Cov.: 32 AF XY: 0.355 AC XY: 26403 AN XY: 74314

African (AFR) AF: 0.202 AC: 8383 AN: 41490

American (AMR) AF: 0.369 AC: 5634 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1290 AN: 5166

South Asian (SAS) AF: 0.270 AC: 1304 AN: 4824

European-Finnish (FIN) AF: 0.498 AC: 5254 AN: 10560

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29632 AN: 67980

Other (OTH) AF: 0.345 AC: 728 AN: 2112

Alfa AF: 0.406 Hom.: 1676

Bravo AF: 0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		-0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs950943;

hg19: chr3-153752226;