rs2236693

Variant names:

• chr21-41800831-G-C
• rs2236693
• NM_001040424.3:c.*409C>G

Your query was ambiguous. Multiple possible variants found:

• chr21-41800831-G-C
• chr21-41800831-G-A

Variant summary

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

The NM_001040424.3(PRDM15):​c.*409C>G variant causes a 3 prime UTR 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. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PRDM15 NM_001040424.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 5 publications found

Genes affected

PRDM15 (HGNC:13999): (PR/SET domain 15) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and promoter-specific chromatin binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II; regulation of signal transduction; and regulation of stem cell division. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040424.3. 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
	PRDM15	NM_001040424.3	MANE Select	c.*409C>G		3_prime_UTR	Exon 24 of 24	NP_001035514.2	P57071-7
	PRDM15	NM_022115.7		c.*409C>G		3_prime_UTR	Exon 31 of 31	NP_071398.5
	PRDM15	NM_001282934.2		c.*409C>G		3_prime_UTR	Exon 25 of 25	NP_001269863.2	P57071-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDM15	ENST00000398548.6	TSL:1 MANE Select	c.*409C>G		3_prime_UTR	Exon 24 of 24	ENSP00000381556.2	P57071-7
	PRDM15	ENST00000422911.6	TSL:1	c.*409C>G		3_prime_UTR	Exon 25 of 25	ENSP00000408592.2	P57071-2
	PRDM15	ENST00000441787.5	TSL:1	n.*2286C>G		non_coding_transcript_exon	Exon 24 of 24	ENSP00000387958.1	Q4W8S1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 13626 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6778

African (AFR) AF: 0.00 AC: 0 AN: 564

American (AMR) AF: 0.00 AC: 0 AN: 590

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 494

East Asian (EAS) AF: 0.00 AC: 0 AN: 532

South Asian (SAS) AF: 0.00 AC: 0 AN: 210

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 560

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 72

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 9740

Other (OTH) AF: 0.00 AC: 0 AN: 864

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.44
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2236693; hg19: chr21-43220991;