chr6-119544976-C-T

Variant names:

• chr6-119544976-C-T
• rs1392089
• ENST00000690557.2:n.64-4832C>T

Variant summary

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

The ENST00000690557.2(ENSG00000287100):​n.64-4832C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0676 in 152,274 control chromosomes in the GnomAD database, including 510 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 0.068 (510 hom., cov: 33)
• Consequence: ENSG00000287100 ENST00000690557.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 5 publications found

Genes affected

ENSG00000287100 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287100	ENST00000690557.2	n.64-4832C>T		intron_variant	Intron 1 of 3
ENSG00000287100	ENST00000692359.3	n.92-4832C>T		intron_variant	Intron 1 of 3
ENSG00000287100	ENST00000701050.2	n.77-4832C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0677 AC: 10294 AN: 152156 Hom.: 511 Cov.: 33

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0740

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

GnomAD4 genome AF: 0.0676 AC: 10288 AN: 152274 Hom.: 510 Cov.: 33 AF XY: 0.0649 AC XY: 4830 AN XY: 74442

African (AFR) AF: 0.0162 AC: 675 AN: 41566

American (AMR) AF: 0.0551 AC: 844 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0778 AC: 375 AN: 4820

European-Finnish (FIN) AF: 0.0626 AC: 663 AN: 10596

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7003 AN: 68012

Other (OTH) AF: 0.0737 AC: 156 AN: 2116

Alfa AF: 0.0902 Hom.: 2167

Bravo AF: 0.0635

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.69
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1392089; hg19: chr6-119866141;