22-41288804-G-C

Variant summary

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

The NM_001317930.2(RANGAP1):c.-38-7722C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,776 control chromosomes in the GnomAD database, including 12,596 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 0.40 (12596 hom., cov: 30)
• Consequence: RANGAP1 NM_001317930.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810

Genes affected

RANGAP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RANGAP1	NM_001317930.2	c.-38-7722C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60375 AN: 151658 Hom.: 12592 Cov.: 30

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.398 AC: 60391 AN: 151776 Hom.: 12596 Cov.: 30 AF XY: 0.393 AC XY: 29202 AN XY: 74214

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.389

Alfa AF: 0.325 Hom.: 971

Bravo AF: 0.375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.9
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1003619; hg19: chr22-41684808;