rs768023

Variant names:

• chr6-108554799-G-A
• rs768023
• ENST00000659932.2:n.136+3365C>T

Variant summary

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

The ENST00000659932.2(ENSG00000287044):​n.136+3365C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,002 control chromosomes in the GnomAD database, including 20,830 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 0.49 (20830 hom., cov: 31)
• Consequence: ENSG00000287044 ENST00000659932.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 20 publications found

Genes affected

ENSG00000287044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659932.2. 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
	ENSG00000287044	ENST00000659932.2		n.136+3365C>T		intron	N/A
	ENSG00000287044	ENST00000784390.1		n.119+3365C>T		intron	N/A
	ENSG00000287044	ENST00000784391.1		n.126+3365C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73966 AN: 151884 Hom.: 20828 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.487 AC: 73992 AN: 152002 Hom.: 20830 Cov.: 31 AF XY: 0.488 AC XY: 36274 AN XY: 74324

African (AFR) AF: 0.185 AC: 7688 AN: 41454

American (AMR) AF: 0.583 AC: 8913 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2171 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3543 AN: 5178

South Asian (SAS) AF: 0.456 AC: 2201 AN: 4826

European-Finnish (FIN) AF: 0.568 AC: 5978 AN: 10528

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41637 AN: 67960

Other (OTH) AF: 0.501 AC: 1053 AN: 2102

Alfa AF: 0.525 Hom.: 2878

Bravo AF: 0.480

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.034
DANN	Benign	0.40
PhyloP100		-1.1

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: rs768023;

hg19: chr6-108876002;