9-120873843-C-G

Variant names:

• chr9-120873843-C-G
• rs10985070
• NM_015651.3:c.268+136G>C

Variant summary

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

The NM_015651.3(PHF19):​c.268+136G>C variant causes a intron 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: 33)
  • Exomes 𝑓: 0.0000021 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PHF19 NM_015651.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 55 publications found

Genes affected

PHF19 (HGNC:24566): (PHD finger protein 19) Enables methylated histone binding activity. Involved in positive regulation of histone H3-K27 methylation. Colocalizes with ESC/E(Z) complex. [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=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015651.3. 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
	PHF19	NM_015651.3	MANE Select	c.268+136G>C		intron	N/A	NP_056466.1	Q5T6S3-1
	PHF19	NM_001286840.1		c.325+136G>C		intron	N/A	NP_001273769.1	A0A087X169
	PHF19	NM_001009936.3		c.268+136G>C		intron	N/A	NP_001009936.1	Q5T6S3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF19	ENST00000373896.8	TSL:2 MANE Select	c.268+136G>C		intron	N/A	ENSP00000363003.3	Q5T6S3-1
	PHF19	ENST00000616568.5	TSL:1	c.325+136G>C		intron	N/A	ENSP00000483946.1	A0A087X169
	PHF19	ENST00000312189.10	TSL:1	c.268+136G>C		intron	N/A	ENSP00000310372.6	Q5T6S3-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000208 AC: 1 AN: 480074 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 255356

African (AFR) AF: 0.00 AC: 0 AN: 13360

American (AMR) AF: 0.00 AC: 0 AN: 20968

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13572

East Asian (EAS) AF: 0.00 AC: 0 AN: 32852

South Asian (SAS) AF: 0.00 AC: 0 AN: 48954

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46242

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2278

European-Non Finnish (NFE) AF: 0.00000363 AC: 1 AN: 275634

Other (OTH) AF: 0.00 AC: 0 AN: 26214

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 41175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.0
DANN	Benign	0.62
PhyloP100		0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10985070; hg19: chr9-123636121;