rs9595049

Variant names:

• chr13-44019775-G-T
• rs9595049
• ENST00000627615.1:n.*784-2700G>T

Variant summary

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

The ENST00000627615.1(ENSG00000281883):​n.*784-2700G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,092 control chromosomes in the GnomAD database, including 8,057 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 0.29 (8057 hom., cov: 32)
• Consequence: ENSG00000281883 ENST00000627615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 6 publications found

Genes affected

ENSG00000281883 (HGNC:):

NRAD1 (HGNC:26981): (non-coding RNA in the aldehyde dehydrogenase 1A pathway)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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
ENSG00000281883	ENST00000627615.1	n.*784-2700G>T		intron_variant	Intron 9 of 12	5		ENSP00000486083.1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44261 AN: 151974 Hom.: 8060 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.291 AC: 44246 AN: 152092 Hom.: 8057 Cov.: 32 AF XY: 0.287 AC XY: 21323 AN XY: 74330

African (AFR) AF: 0.0800 AC: 3320 AN: 41520

American (AMR) AF: 0.238 AC: 3636 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1156 AN: 3472

East Asian (EAS) AF: 0.179 AC: 926 AN: 5174

South Asian (SAS) AF: 0.312 AC: 1499 AN: 4808

European-Finnish (FIN) AF: 0.415 AC: 4386 AN: 10556

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28349 AN: 67968

Other (OTH) AF: 0.293 AC: 618 AN: 2106

Alfa AF: 0.373 Hom.: 15439

Bravo AF: 0.270

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.64
PhyloP100		0.044

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

Other links and lift over

dbSNP: rs9595049; hg19: chr13-44593911;