chr6-23518043-T-C

Variant names:

• chr6-23518043-T-C
• rs9295592
• ENST00000690652.3:n.356-60373A>G

Variant summary

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

The ENST00000690652.3(ENSG00000289368):​n.356-60373A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,948 control chromosomes in the GnomAD database, including 23,138 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 0.55 (23138 hom., cov: 31)
• Consequence: ENSG00000289368 ENST00000690652.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 3 publications found

Genes affected

ENSG00000289368 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690652.3. 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
	ENSG00000289368	ENST00000690652.3		n.356-60373A>G		intron	N/A
	ENSG00000289368	ENST00000700866.2		n.181-60373A>G		intron	N/A
	ENSG00000289368	ENST00000702216.2		n.203-60373A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83306 AN: 151830 Hom.: 23105 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.549 AC: 83394 AN: 151948 Hom.: 23138 Cov.: 31 AF XY: 0.545 AC XY: 40479 AN XY: 74260

African (AFR) AF: 0.600 AC: 24851 AN: 41440

American (AMR) AF: 0.473 AC: 7213 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2238 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1748 AN: 5148

South Asian (SAS) AF: 0.488 AC: 2347 AN: 4808

European-Finnish (FIN) AF: 0.550 AC: 5810 AN: 10556

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37381 AN: 67956

Other (OTH) AF: 0.545 AC: 1151 AN: 2110

Alfa AF: 0.541 Hom.: 9324

Bravo AF: 0.543

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.59
PhyloP100		-0.12

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: rs9295592;

hg19: chr6-23518271;

COSMIC: COSV66848353;