17-12786824-T-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP44-AS1	NR_104607.1	n.142+3319A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP44-AS1	ENST00000584772.1	n.100+3319A>C		intron_variant	Intron 1 of 1	1

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

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.395

Alfa AF: 0.279 Hom.: 10738

Bravo AF: 0.439

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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