rs12142

Variant names:

• chr4-37610904-G-A
• rs12142
• NM_001085400.2:c.*2442C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-37610904-G-A
• chr4-37610904-G-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.*2442C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,076 control chromosomes in the GnomAD database, including 8,189 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 0.29 (8189 hom., cov: 33)
• Consequence: RELL1 NM_001085400.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 12 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]

C4orf19 (HGNC:25618): (chromosome 4 open reading frame 19) Located in cell junction and nucleoplasm. [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 = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RELL1	NM_001085400.2	c.*2442C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000454158.7	NP_001078869.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RELL1	ENST00000454158.7	c.*2442C>T		3_prime_UTR_variant	Exon 7 of 7	5	NM_001085400.2	ENSP00000398778.2
RELL1	ENST00000314117.8	c.*4-19687C>T		intron_variant	Intron 6 of 6	1		ENSP00000313385.4
C4orf19	ENST00000508175.5	c.33-11921G>A		intron_variant	Intron 3 of 3	3		ENSP00000421537.1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44372 AN: 151958 Hom.: 8191 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.292 AC: 44371 AN: 152076 Hom.: 8189 Cov.: 33 AF XY: 0.293 AC XY: 21753 AN XY: 74312

African (AFR) AF: 0.107 AC: 4459 AN: 41496

American (AMR) AF: 0.227 AC: 3477 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3470

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5186

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4826

European-Finnish (FIN) AF: 0.478 AC: 5037 AN: 10532

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27348 AN: 67962

Other (OTH) AF: 0.288 AC: 609 AN: 2114

Alfa AF: 0.354 Hom.: 12704

Bravo AF: 0.262

Asia WGS AF: 0.164 AC: 570 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.73
PhyloP100		-0.75
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: rs12142; hg19: chr4-37612526;