rs13144232

chr4-37645612-G-A

Variant summary

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

The NM_001085400.2(RELL1):c.385+1756C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,084 control chromosomes in the GnomAD database, including 7,695 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 0.31 (7695 hom., cov: 32)
• Consequence: RELL1 NM_001085400.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

Genes affected

RELL1 (HGNC:27379): (RELT like 1) Involved in positive regulation of p38MAPK cascade. Located in microtubule cytoskeleton and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RELL1	NM_001085400.2	c.385+1756C>T		intron_variant		ENST00000454158.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RELL1	ENST00000454158.7	c.385+1756C>T		intron_variant		5	NM_001085400.2	P1
RELL1	ENST00000314117.8	c.385+1756C>T		intron_variant		1		P1
RELL1	ENST00000512114.1	c.448+1756C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47822 AN: 151966 Hom.: 7695 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.315 AC: 47843 AN: 152084 Hom.: 7695 Cov.: 32 AF XY: 0.307 AC XY: 22857 AN XY: 74346

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.324

Alfa AF: 0.343 Hom.: 1892

Bravo AF: 0.314

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.44

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

Publications

LitVar

Other links and lift over

dbSNP: rs13144232; hg19: chr4-37647234;