9-95529368-T-G

Variant names:

• chr9-95529368-T-G
• rs16909952
• ENST00000810379.1:n.248-3238A>C

Variant summary

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

The ENST00000810379.1(ENSG00000305315):​n.248-3238A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0861 in 152,258 control chromosomes in the GnomAD database, including 1,623 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 0.086 (1623 hom., cov: 32)
• Consequence: ENSG00000305315 ENST00000810379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471
• Publications: 0 publications found

Genes affected

ENSG00000305315 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810379.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305315	ENST00000810379.1		n.248-3238A>C		intron	N/A
	ENSG00000305315	ENST00000810380.1		n.497-6071A>C		intron	N/A
	ENSG00000305315	ENST00000810381.1		n.333-6071A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0859 AC: 13064 AN: 152140 Hom.: 1605 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.0928

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.000941

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00664

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0861 AC: 13113 AN: 152258 Hom.: 1623 Cov.: 32 AF XY: 0.0846 AC XY: 6296 AN XY: 74462

African (AFR) AF: 0.271 AC: 11241 AN: 41514

American (AMR) AF: 0.0352 AC: 539 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00923 AC: 32 AN: 3468

East Asian (EAS) AF: 0.0926 AC: 480 AN: 5182

South Asian (SAS) AF: 0.0344 AC: 166 AN: 4820

European-Finnish (FIN) AF: 0.000941 AC: 10 AN: 10624

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00663 AC: 451 AN: 68024

Other (OTH) AF: 0.0757 AC: 160 AN: 2114

Alfa AF: 0.0532 Hom.: 107

Bravo AF: 0.0970

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		-0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16909952;

hg19: chr9-98291650;