chr3-101868949-T-A

Variant names:

• chr3-101868949-T-A
• rs694936
• ENST00000772040.1:n.137+156T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000772040.1(RDUR):​n.137+156T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,056 control chromosomes in the GnomAD database, including 10,561 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 0.36 (10561 hom., cov: 32)
• Consequence: RDUR ENST00000772040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 5 publications found

Genes affected

RDUR (HGNC:27190): (RIG-I dependent antiviral response regulator RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772040.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RDUR	ENST00000772040.1		n.137+156T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54872 AN: 151938 Hom.: 10560 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.361 AC: 54884 AN: 152056 Hom.: 10561 Cov.: 32 AF XY: 0.353 AC XY: 26227 AN XY: 74322

African (AFR) AF: 0.247 AC: 10254 AN: 41484

American (AMR) AF: 0.312 AC: 4763 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1607 AN: 3466

East Asian (EAS) AF: 0.394 AC: 2035 AN: 5166

South Asian (SAS) AF: 0.320 AC: 1542 AN: 4824

European-Finnish (FIN) AF: 0.320 AC: 3384 AN: 10562

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 30059 AN: 67960

Other (OTH) AF: 0.370 AC: 778 AN: 2102

Alfa AF: 0.381 Hom.: 1426

Bravo AF: 0.362

Asia WGS AF: 0.306 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.73
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs694936; hg19: chr3-101587793;