rs34229995

Variant names:

• chr6-15243787-C-G
• rs34229995
• ENST00000607711.1:n.*136G>C

Variant summary

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

The ENST00000607711.1(JARID2-DT):​n.*136G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 152,258 control chromosomes in the GnomAD database, including 61 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 0.020 (61 hom., cov: 32)
  • Exomes 𝑓: 0.056 (0 hom.)
• Consequence: JARID2-DT ENST00000607711.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 8 publications found

Genes affected

JARID2-DT (HGNC:55240): (JARID2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAdExome4 highest population allele frequency = 0.0556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JARID2-DT	NR_187237.1	n.*136G>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JARID2-DT	ENST00000607711.1	n.*136G>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0203 AC: 3088 AN: 152122 Hom.: 61 Cov.: 32

Gnomad AFR AF: 0.00355

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.00982

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.00643

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0247

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.0556 AC: 1 AN: 18 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.0833 AC: 1 AN: 12

GnomAD4 genome AF: 0.0203 AC: 3087 AN: 152240 Hom.: 61 Cov.: 32 AF XY: 0.0227 AC XY: 1689 AN XY: 74430

African (AFR) AF: 0.00354 AC: 147 AN: 41540

American (AMR) AF: 0.00981 AC: 150 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5194

South Asian (SAS) AF: 0.00622 AC: 30 AN: 4820

European-Finnish (FIN) AF: 0.0837 AC: 885 AN: 10578

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0247 AC: 1679 AN: 68020

Other (OTH) AF: 0.0199 AC: 42 AN: 2112

Alfa AF: 0.0267 Hom.: 4

Bravo AF: 0.0143

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.35
DANN	Benign	0.52
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs34229995; hg19: chr6-15244018;