6-90587895-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762879.1. 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
	ENSG00000299366	ENST00000762879.1		n.806C>T		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000299366	ENST00000762880.1		n.636C>T		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000299366	ENST00000762883.1		n.567C>T		non_coding_transcript_exon	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 v4.9

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

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

Other links and lift over

dbSNP: rs9359896;

hg19: chr6-91297614;