rs6739040

Variant names:

• chr2-217087003-A-G
• rs6739040
• ENST00000695932.1:n.509+92985A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-217087003-A-G
• chr2-217087003-A-T

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.509+92985A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,210 control chromosomes in the GnomAD database, including 1,548 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 0.12 (1548 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.509+92985A>G		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.173-66408A>G		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18172 AN: 152092 Hom.: 1544 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.120 AC: 18207 AN: 152210 Hom.: 1548 Cov.: 32 AF XY: 0.117 AC XY: 8697 AN XY: 74420

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.0974

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.0261

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0718

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0821 Hom.: 923

Bravo AF: 0.127

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6739040; hg19: chr2-217951726;