2-217043749-A-G

Position:

• chr2-217043749-A-G

Variant summary

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

The variant allele was found at a frequency of 0.401 in 152,062 control chromosomes in the GnomAD database, including 12,718 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 (12718 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.217043749A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.509+49731A>G		intron_variant
DIRC3-AS1	ENST00000695934.1	n.172+49731A>G		intron_variant
DIRC3-AS1	ENST00000695937.1	n.289+6469A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60993 AN: 151944 Hom.: 12705 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.401 AC: 61048 AN: 152062 Hom.: 12718 Cov.: 32 AF XY: 0.392 AC XY: 29132 AN XY: 74328

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.404

Alfa AF: 0.379 Hom.: 6200

Bravo AF: 0.406

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.49
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490444; hg19: chr2-217908472;