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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376157	XR_930138.3	n.619-3238A>C		intron_variant	Intron 2 of 3
LOC105376157	XR_930139.3	n.586-3238A>C		intron_variant	Intron 3 of 4
LOC105376157	XR_930140.3	n.619-6071A>C		intron_variant	Intron 2 of 2
LOC105376157	XR_930141.3	n.407-3238A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305315	ENST00000810379.1	n.248-3238A>C		intron_variant	Intron 1 of 2
ENSG00000305315	ENST00000810380.1	n.497-6071A>C		intron_variant	Intron 2 of 2
ENSG00000305315	ENST00000810381.1	n.333-6071A>C		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs16909952; hg19: chr9-98291650;