9-34771856-A-T

Position:

• chr9-34771856-A-T

Variant summary

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

The ENST00000664167.1(ENSG00000288583):​n.87-2183A>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 0.131 in 152,212 control chromosomes in the GnomAD database, including 2,106 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 0.13 (2106 hom., cov: 32)
• Consequence: ENST00000664167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+68818A>T		intron_variant			XP_047279058.1
PHF24	XM_047423103.1	c.70+68818A>T		intron_variant			XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664167.1	n.87-2183A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19980 AN: 152094 Hom.: 2107 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.131 AC: 19980 AN: 152212 Hom.: 2106 Cov.: 32 AF XY: 0.137 AC XY: 10184 AN XY: 74422

Gnomad4 AFR AF: 0.0474

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.148

Alfa AF: 0.121 Hom.: 166

Bravo AF: 0.130

Asia WGS AF: 0.381 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16931907; hg19: chr9-34771853;