11-65663889-C-T

Position:

• chr11-65663889-C-T

Variant summary

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

The NR_183625.1(RELA-DT):​n.143+741C>T 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 0.168 in 152,180 control chromosomes in the GnomAD database, including 2,672 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 0.17 (2672 hom., cov: 31)
• Consequence: RELA-DT NR_183625.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

Genes affected

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

RELA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RELA-DT	NR_183625.1	n.143+741C>T		intron_variant, non_coding_transcript_variant
RELA	NM_001404662.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RELA-DT	ENST00000691526.2	n.161+741C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25587 AN: 152062 Hom.: 2666 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.0937

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.168 AC: 25610 AN: 152180 Hom.: 2672 Cov.: 31 AF XY: 0.169 AC XY: 12599 AN XY: 74416

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.0942

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.160

Alfa AF: 0.137 Hom.: 2462

Bravo AF: 0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7101916; hg19: chr11-65431360;