4-37643767-C-T

Variant names:

• chr4-37643767-C-T
• rs4832928
• NM_001085400.2:c.385+3601G>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+3601G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,034 control chromosomes in the GnomAD database, including 6,768 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 0.30 (6768 hom., cov: 32)
• Consequence: RELL1 NM_001085400.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RELL1	NM_001085400.2	c.385+3601G>A		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+3601G>A		intron_variant	Intron 3 of 6	5	NM_001085400.2	ENSP00000398778.2
RELL1	ENST00000314117.8	c.385+3601G>A		intron_variant	Intron 3 of 6	1		ENSP00000313385.4
RELL1	ENST00000512114.1	c.448+3601G>A		intron_variant	Intron 3 of 4	3		ENSP00000424031.1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44870 AN: 151916 Hom.: 6769 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.295 AC: 44897 AN: 152034 Hom.: 6768 Cov.: 32 AF XY: 0.293 AC XY: 21782 AN XY: 74302

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.313

Alfa AF: 0.313 Hom.: 5326

Bravo AF: 0.305

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.3
DANN	Benign	0.59

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: rs4832928; hg19: chr4-37645389;