2-98849039-A-G

Position:

• chr2-98849039-A-G

Variant summary

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

The NM_207362.3(CRACDL):​c.-10-2229T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,114 control chromosomes in the GnomAD database, including 29,536 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 0.61 (29536 hom., cov: 33)
• Consequence: CRACDL NM_207362.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

Genes affected

CRACDL (HGNC:33454): (CRACD like)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRACDL	NM_207362.3	c.-10-2229T>C		intron_variant		ENST00000397899.7	NP_997245.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRACDL	ENST00000397899.7	c.-10-2229T>C		intron_variant		1	NM_207362.3	ENSP00000380996	P1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92387 AN: 151994 Hom.: 29496 Cov.: 33

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.608 AC: 92484 AN: 152114 Hom.: 29536 Cov.: 33 AF XY: 0.601 AC XY: 44651 AN XY: 74356

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.609

Alfa AF: 0.549 Hom.: 29280

Bravo AF: 0.630

Asia WGS AF: 0.456 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6733011; hg19: chr2-99465502;