rs10513455

Variant names:

• chr3-154070693-G-A
• rs10513455
• ENST00000491862.6:n.357+37976C>T

Variant summary

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

The ENST00000491862.6(ARHGEF26-AS1):​n.357+37976C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 152,134 control chromosomes in the GnomAD database, including 385 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 0.046 (385 hom., cov: 32)
• Consequence: ARHGEF26-AS1 ENST00000491862.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGEF26-AS1	NR_037901.1	n.256+37976C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGEF26-AS1	ENST00000491862.6	n.357+37976C>T		intron_variant	Intron 2 of 3	1
ARHGEF26-AS1	ENST00000467912.6	n.360-40314C>T		intron_variant	Intron 2 of 3	3
ARHGEF26-AS1	ENST00000479270.6	n.378+37976C>T		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7031 AN: 152016 Hom.: 383 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.00560

Gnomad FIN AF: 0.00302

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00816

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0464 AC: 7061 AN: 152134 Hom.: 385 Cov.: 32 AF XY: 0.0451 AC XY: 3355 AN XY: 74396

African (AFR) AF: 0.130 AC: 5383 AN: 41482

American (AMR) AF: 0.0255 AC: 390 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3466

East Asian (EAS) AF: 0.111 AC: 577 AN: 5186

South Asian (SAS) AF: 0.00560 AC: 27 AN: 4820

European-Finnish (FIN) AF: 0.00302 AC: 32 AN: 10598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00816 AC: 555 AN: 67994

Other (OTH) AF: 0.0369 AC: 78 AN: 2112

Alfa AF: 0.0307 Hom.: 62

Bravo AF: 0.0519

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.50
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs10513455; hg19: chr3-153788482;