rs1432295

Variant names:

• chr2-60839531-G-A
• rs1432295
• ENST00000439412.6:n.403+4526C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-60839531-G-A
• chr2-60839531-G-C
• chr2-60839531-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439412.6(REL-DT):​n.403+4526C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,056 control chromosomes in the GnomAD database, including 37,430 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 0.69 (37430 hom., cov: 31)
• Consequence: REL-DT ENST00000439412.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 51 publications found

Genes affected

REL-DT (HGNC:49572): (REL divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439412.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REL-DT	ENST00000439412.6	TSL:4	n.403+4526C>T		intron	N/A
	REL-DT	ENST00000748843.1		n.363+4526C>T		intron	N/A
	REL-DT	ENST00000748844.1		n.248+4526C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104876 AN: 151938 Hom.: 37375 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.690 AC: 104991 AN: 152056 Hom.: 37430 Cov.: 31 AF XY: 0.695 AC XY: 51620 AN XY: 74314

African (AFR) AF: 0.811 AC: 33673 AN: 41496

American (AMR) AF: 0.727 AC: 11102 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2422 AN: 3468

East Asian (EAS) AF: 0.979 AC: 5072 AN: 5180

South Asian (SAS) AF: 0.884 AC: 4265 AN: 4826

European-Finnish (FIN) AF: 0.567 AC: 5966 AN: 10530

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40343 AN: 67962

Other (OTH) AF: 0.665 AC: 1406 AN: 2114

Alfa AF: 0.634 Hom.: 140760

Bravo AF: 0.705

Asia WGS AF: 0.920 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.52
PhyloP100		-0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1432295;

hg19: chr2-61066666;