4-37643767-C-T

Variant names:

• chr4-37643767-C-T
• rs4832928
• NM_001085400.2:c.385+3601G>A

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+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
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001085400.2. 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
	RELL1	NM_001085400.2	MANE Select	c.385+3601G>A		intron	N/A	NP_001078869.1	Q8IUW5
	RELL1	NM_001085399.2		c.385+3601G>A		intron	N/A	NP_001078868.1	Q8IUW5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RELL1	ENST00000454158.7	TSL:5 MANE Select	c.385+3601G>A		intron	N/A	ENSP00000398778.2	Q8IUW5
	RELL1	ENST00000314117.8	TSL:1	c.385+3601G>A		intron	N/A	ENSP00000313385.4	Q8IUW5
	RELL1	ENST00000858689.1		c.385+3601G>A		intron	N/A	ENSP00000528748.1

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

African (AFR) AF: 0.234 AC: 9719 AN: 41462

American (AMR) AF: 0.346 AC: 5290 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2177 AN: 5166

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4820

European-Finnish (FIN) AF: 0.240 AC: 2532 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21245 AN: 67956

Other (OTH) AF: 0.313 AC: 657 AN: 2100

Alfa AF: 0.315 Hom.: 19627

Bravo AF: 0.305

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.3
DANN	Benign	0.59
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: rs4832928; hg19: chr4-37645389;