ENST00000702683.2:n.300C>G

Variant names:

• chr1-3068848-G-C
• rs2472818
• ENST00000702683.2:n.300C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000702683.2(PRDM16-DT):​n.300C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: PRDM16-DT ENST00000702683.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 0 publications found

Genes affected

PRDM16-DT (HGNC:48664): (PRDM16 divergent transcript)

LOC124903827 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903827	XM_047436534.1	c.*100C>G		3_prime_UTR_variant	Exon 2 of 7		XP_047292490.1
LOC124903827	XM_047436535.1	c.*100C>G		3_prime_UTR_variant	Exon 2 of 6		XP_047292491.1
LOC124903827	XM_047436536.1	c.*100C>G		3_prime_UTR_variant	Exon 2 of 8		XP_047292492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDM16-DT	ENST00000702683.2	n.300C>G		non_coding_transcript_exon_variant	Exon 1 of 1
PRDM16-DT	ENST00000818119.1	n.202C>G		non_coding_transcript_exon_variant	Exon 2 of 2
PRDM16-DT	ENST00000687743.2	n.232+18C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	18
DANN	Benign	0.63
PhyloP100		2.0
PromoterAI		-0.038	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2472818; hg19: chr1-2985412;