rs1074156

Variant names:

• chr11-65690698-G-T
• rs1074156
• ENST00000820174.1:n.485+2925G>T

Variant summary

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

The ENST00000820174.1(RELA-DT):​n.485+2925G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,964 control chromosomes in the GnomAD database, including 8,874 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 0.34 (8874 hom., cov: 31)
• Consequence: RELA-DT ENST00000820174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 12 publications found

Genes affected

RELA-DT (HGNC:54185): (RELA divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820174.1. 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
	RELA-DT	ENST00000820174.1		n.485+2925G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50942 AN: 151846 Hom.: 8869 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.335 AC: 50983 AN: 151964 Hom.: 8874 Cov.: 31 AF XY: 0.340 AC XY: 25214 AN XY: 74260

African (AFR) AF: 0.323 AC: 13365 AN: 41432

American (AMR) AF: 0.248 AC: 3784 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1087 AN: 5166

South Asian (SAS) AF: 0.326 AC: 1570 AN: 4822

European-Finnish (FIN) AF: 0.481 AC: 5070 AN: 10548

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23846 AN: 67958

Other (OTH) AF: 0.321 AC: 678 AN: 2110

Alfa AF: 0.340 Hom.: 1560

Bravo AF: 0.313

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.56
DANN	Benign	0.22
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1074156;

hg19: chr11-65458169;