rs13144232

Variant names:

• chr4-37645612-G-A
• rs13144232
• NM_001085400.2:c.385+1756C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RELL1	NM_001085400.2	c.385+1756C>T		intron_variant	Intron 3 of 6	ENST00000454158.7	NP_001078869.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RELL1	ENST00000454158.7	c.385+1756C>T		intron_variant	Intron 3 of 6	5	NM_001085400.2	ENSP00000398778.2
RELL1	ENST00000314117.8	c.385+1756C>T		intron_variant	Intron 3 of 6	1		ENSP00000313385.4
RELL1	ENST00000512114.1	c.448+1756C>T		intron_variant	Intron 3 of 4	3		ENSP00000424031.1

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

African (AFR) AF: 0.246 AC: 10207 AN: 41490

American (AMR) AF: 0.272 AC: 4153 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1462 AN: 3464

East Asian (EAS) AF: 0.284 AC: 1469 AN: 5172

South Asian (SAS) AF: 0.281 AC: 1356 AN: 4820

European-Finnish (FIN) AF: 0.275 AC: 2903 AN: 10570

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25135 AN: 67972

Other (OTH) AF: 0.324 AC: 685 AN: 2114

Alfa AF: 0.314 Hom.: 3596

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
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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: rs13144232; hg19: chr4-37647234;