rs1549738

Positions:

• chr2-217253999-G-A
• chr2-217253999-G-T

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.510-7661G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,144 control chromosomes in the GnomAD database, including 46,284 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 0.77 (46284 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

DIRC3-AS1 (HGNC:50636): (DIRC3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.510-7661G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.714-5305G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695940.1	n.581-5305G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116793 AN: 152026 Hom.: 46268 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.768 AC: 116848 AN: 152144 Hom.: 46284 Cov.: 32 AF XY: 0.764 AC XY: 56845 AN XY: 74378

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.784

Alfa AF: 0.795 Hom.: 8858

Bravo AF: 0.756

Asia WGS AF: 0.679 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.099
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1549738; hg19: chr2-218118722;