rs2024566

chr22-41301334-A-G

Variant summary

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

The NM_001317930.2(RANGAP1):c.-39+699T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,002 control chromosomes in the GnomAD database, including 7,131 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 0.28 (7131 hom., cov: 32)
• Consequence: RANGAP1 NM_001317930.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

Genes affected

RANGAP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RANGAP1	NM_001317930.2	c.-39+699T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43111 AN: 151884 Hom.: 7115 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.284 AC: 43143 AN: 152002 Hom.: 7131 Cov.: 32 AF XY: 0.291 AC XY: 21603 AN XY: 74296

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0734

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.306

Alfa AF: 0.313 Hom.: 9964

Bravo AF: 0.292

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.7
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2024566; hg19: chr22-41697338;