rs950943

Positions:

• chr3-154034437-A-T

Variant summary

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

The NR_037901.1(ARHGEF26-AS1):​n.257-4061T>A variant causes a intron, non coding transcript 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 NR_037901.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGEF26-AS1	NR_037901.1	n.257-4061T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGEF26-AS1	ENST00000480639.6	n.400-4058T>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.345

Alfa AF: 0.406 Hom.: 1676

Bravo AF: 0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs950943; hg19: chr3-153752226;