rs7233739

Variant names:

• chr18-6728489-G-A
• rs7233739
• ENST00000577327.2:n.930C>T

Variant summary

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

The ENST00000577327.2(ARHGAP28-AS1):​n.930C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,072 control chromosomes in the GnomAD database, including 21,864 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 0.53 (21864 hom., cov: 33)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: ARHGAP28-AS1 ENST00000577327.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 5 publications found

Genes affected

ARHGAP28-AS1 (HGNC:55320): (ARHGAP28 antisense RNA 1)

ENSG00000279479 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP28-AS1	ENST00000577327.2	n.930C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2
ENSG00000279479	ENST00000623844.1	n.1437G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.533 AC: 81027 AN: 151948 Hom.: 21822 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

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: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.533 AC: 81124 AN: 152066 Hom.: 21864 Cov.: 33 AF XY: 0.536 AC XY: 39849 AN XY: 74332

African (AFR) AF: 0.541 AC: 22453 AN: 41486

American (AMR) AF: 0.566 AC: 8649 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2039 AN: 3472

East Asian (EAS) AF: 0.452 AC: 2333 AN: 5164

South Asian (SAS) AF: 0.708 AC: 3412 AN: 4820

European-Finnish (FIN) AF: 0.496 AC: 5233 AN: 10550

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35144 AN: 67992

Other (OTH) AF: 0.530 AC: 1118 AN: 2110

Alfa AF: 0.534 Hom.: 3775

Bravo AF: 0.534

Asia WGS AF: 0.583 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.32
DANN	Benign	0.61
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7233739; hg19: chr18-6728488;