rs9359896

Variant names:

• chr6-90587895-C-T
• rs9359896
• ENST00000762879.1:n.806C>T

Variant summary

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

The ENST00000762879.1(ENSG00000299366):​n.806C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0595 in 152,266 control chromosomes in the GnomAD database, including 476 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 0.060 (476 hom., cov: 32)
• Consequence: ENSG00000299366 ENST00000762879.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 1 publications found

Genes affected

ENSG00000299366 (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 = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901363	XR_007059679.1	n.548C>T		non_coding_transcript_exon_variant	Exon 2 of 3
LOC124901363	XR_007059680.1	n.1102C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124901363	XR_007059681.1	n.557+148C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299366	ENST00000762879.1	n.806C>T		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000299366	ENST00000762880.1	n.636C>T		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000299366	ENST00000762883.1	n.567C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0594 AC: 9035 AN: 152148 Hom.: 472 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.00698

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0290

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0595 AC: 9060 AN: 152266 Hom.: 476 Cov.: 32 AF XY: 0.0584 AC XY: 4351 AN XY: 74464

African (AFR) AF: 0.134 AC: 5567 AN: 41522

American (AMR) AF: 0.0509 AC: 779 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3472

East Asian (EAS) AF: 0.0349 AC: 181 AN: 5186

South Asian (SAS) AF: 0.0441 AC: 213 AN: 4830

European-Finnish (FIN) AF: 0.00698 AC: 74 AN: 10606

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0290 AC: 1974 AN: 68032

Other (OTH) AF: 0.0659 AC: 139 AN: 2108

Alfa AF: 0.0526 Hom.: 57

Bravo AF: 0.0668

Asia WGS AF: 0.0670 AC: 235 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	2.4
DANN	Benign	0.59
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs9359896; hg19: chr6-91297614;