rs10985070

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-120873843-C-A
• chr9-120873843-C-G

Variant summary

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

The NM_001286840.1(PHF19):​c.325+136G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 631,026 control chromosomes in the GnomAD database, including 98,079 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 0.48 (19107 hom., cov: 33)
  • Exomes 𝑓: 0.57 (78972 hom.)
• Consequence: PHF19 NM_001286840.1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286840.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF19	NM_015651.3	MANE Select	c.268+136G>T		intron	N/A	NP_056466.1
	PHF19	NM_001286840.1		c.325+136G>T		intron	N/A	NP_001273769.1
	PHF19	NM_001009936.3		c.268+136G>T		intron	N/A	NP_001009936.1

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73032 AN: 151944 Hom.: 19093 Cov.: 33

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.539

GnomAD4 exome AF: 0.567 AC: 271644 AN: 478964 Hom.: 78972 AF XY: 0.577 AC XY: 146923 AN XY: 254798

African (AFR) AF: 0.251 AC: 3345 AN: 13344

American (AMR) AF: 0.597 AC: 12465 AN: 20890

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 8739 AN: 13542

East Asian (EAS) AF: 0.476 AC: 15605 AN: 32774

South Asian (SAS) AF: 0.684 AC: 33407 AN: 48850

European-Finnish (FIN) AF: 0.524 AC: 24172 AN: 46164

Middle Eastern (MID) AF: 0.652 AC: 1482 AN: 2274

European-Non Finnish (NFE) AF: 0.574 AC: 157822 AN: 274980

Other (OTH) AF: 0.559 AC: 14607 AN: 26146

GnomAD4 genome AF: 0.481 AC: 73073 AN: 152062 Hom.: 19107 Cov.: 33 AF XY: 0.487 AC XY: 36189 AN XY: 74310

African (AFR) AF: 0.252 AC: 10435 AN: 41460

American (AMR) AF: 0.578 AC: 8829 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2296 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2566 AN: 5164

South Asian (SAS) AF: 0.672 AC: 3248 AN: 4830

European-Finnish (FIN) AF: 0.540 AC: 5701 AN: 10554

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38254 AN: 67978

Other (OTH) AF: 0.538 AC: 1135 AN: 2110

Alfa AF: 0.527 Hom.: 41175

Bravo AF: 0.472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.9
DANN	Benign	0.60
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

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;