9-34868380-C-T

Position:

• chr9-34868380-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658462.1(ENSG00000287368):​n.141-21199C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,170 control chromosomes in the GnomAD database, including 42,725 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 0.75 (42725 hom., cov: 33)
• Consequence: ENST00000658462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_017014553.3	c.-65-21199C>T		intron_variant			XP_016870042.1
PHF24	XM_017014554.2	c.-65-21199C>T		intron_variant			XP_016870043.1
PHF24	XM_017014555.2	c.-65-21199C>T		intron_variant			XP_016870044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658462.1	n.141-21199C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113578 AN: 152052 Hom.: 42699 Cov.: 33

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.747 AC: 113657 AN: 152170 Hom.: 42725 Cov.: 33 AF XY: 0.747 AC XY: 55555 AN XY: 74392

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.779

Alfa AF: 0.735 Hom.: 4175

Bravo AF: 0.747

Asia WGS AF: 0.785 AC: 2732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13290746; hg19: chr9-34868377; COSMIC: COSV60353226;