ENST00000648572.1:n.991-20730G>A

Variant names:

• chr6-88199164-C-T
• rs10485168
• ENST00000648572.1:n.991-20730G>A

Variant summary

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

The ENST00000648572.1(ENSG00000234426):​n.991-20730G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,130 control chromosomes in the GnomAD database, including 1,282 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 0.12 (1282 hom., cov: 33)
• Consequence: ENSG00000234426 ENST00000648572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 2 publications found

Genes affected

ENSG00000234426 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648572.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234426	ENST00000648572.1		n.991-20730G>A		intron	N/A
	ENSG00000298549	ENST00000756364.1		n.129-12433C>T		intron	N/A
	ENSG00000298549	ENST00000756365.1		n.572-12433C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17840 AN: 152012 Hom.: 1281 Cov.: 33

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.117 AC: 17834 AN: 152130 Hom.: 1282 Cov.: 33 AF XY: 0.117 AC XY: 8721 AN XY: 74342

African (AFR) AF: 0.0616 AC: 2558 AN: 41532

American (AMR) AF: 0.0850 AC: 1299 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3470

East Asian (EAS) AF: 0.0474 AC: 245 AN: 5172

South Asian (SAS) AF: 0.0770 AC: 371 AN: 4816

European-Finnish (FIN) AF: 0.227 AC: 2394 AN: 10548

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10299 AN: 67988

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.129 Hom.: 761

Bravo AF: 0.104

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10485168; hg19: chr6-88908883; COSMIC: COSV69412309;