1-3068848-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000702683.2(PRDM16-DT):​n.300C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 151,974 control chromosomes in the GnomAD database, including 415 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.047 (415 hom., cov: 30)
• Consequence: PRDM16-DT ENST00000702683.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.99
• Publications: 0 publications found

Genes affected

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

LOC124903827 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP6: Variant 1-3068848-G-A is Benign according to our data. Variant chr1-3068848-G-A is described in ClinVar as [Benign]. Clinvar id is 671193.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903827	XM_047436534.1	c.*100C>T		3_prime_UTR_variant	Exon 2 of 7		XP_047292490.1
LOC124903827	XM_047436535.1	c.*100C>T		3_prime_UTR_variant	Exon 2 of 6		XP_047292491.1
LOC124903827	XM_047436536.1	c.*100C>T		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>T		non_coding_transcript_exon_variant	Exon 1 of 1
PRDM16-DT	ENST00000818119.1	n.202C>T		non_coding_transcript_exon_variant	Exon 2 of 2
PRDM16-DT	ENST00000687743.2	n.232+18C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 7104 AN: 151852 Hom.: 414 Cov.: 30

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0486

Gnomad FIN AF: 0.00405

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00521

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0468 AC: 7112 AN: 151974 Hom.: 415 Cov.: 30 AF XY: 0.0468 AC XY: 3473 AN XY: 74272

African (AFR) AF: 0.122 AC: 5052 AN: 41462

American (AMR) AF: 0.0275 AC: 421 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3470

East Asian (EAS) AF: 0.186 AC: 940 AN: 5044

South Asian (SAS) AF: 0.0480 AC: 231 AN: 4814

European-Finnish (FIN) AF: 0.00405 AC: 43 AN: 10616

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00521 AC: 354 AN: 67950

Other (OTH) AF: 0.0275 AC: 58 AN: 2112

Alfa AF: 0.0298 Hom.: 34

Bravo AF: 0.0532

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 16, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	18
DANN	Benign	0.94
PhyloP100		2.0
PromoterAI		-0.10	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;