17-12786824-T-G

Variant names:

• chr17-12786824-T-G
• rs7212848
• ENST00000584772.1:n.100+3319A>C

Variant summary

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

The ENST00000584772.1(ARHGAP44-AS1):​n.100+3319A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,102 control chromosomes in the GnomAD database, including 17,393 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 0.41 (17393 hom., cov: 32)
• Consequence: ARHGAP44-AS1 ENST00000584772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 2 publications found

Genes affected

ARHGAP44-AS1 (HGNC:55326): (ARHGAP44 and MYOCD antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584772.1. 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
	ARHGAP44-AS1	NR_104607.1		n.142+3319A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP44-AS1	ENST00000584772.1	TSL:1	n.100+3319A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62877 AN: 151984 Hom.: 17334 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.414 AC: 63000 AN: 152102 Hom.: 17393 Cov.: 32 AF XY: 0.412 AC XY: 30625 AN XY: 74368

African (AFR) AF: 0.789 AC: 32730 AN: 41502

American (AMR) AF: 0.332 AC: 5069 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1914 AN: 5158

South Asian (SAS) AF: 0.366 AC: 1761 AN: 4816

European-Finnish (FIN) AF: 0.222 AC: 2341 AN: 10564

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16805 AN: 67998

Other (OTH) AF: 0.395 AC: 833 AN: 2110

Alfa AF: 0.314 Hom.: 25292

Bravo AF: 0.439

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.70
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs7212848; hg19: chr17-12690141; COSMIC: COSV52391241;