rs754387

Variant names:

• chr6-88169140-A-C
• rs754387
• ENST00000756364.1:n.129-42457A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-88169140-A-C
• chr6-88169140-A-G

Variant summary

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

The ENST00000756364.1(ENSG00000298549):​n.129-42457A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 152,006 control chromosomes in the GnomAD database, including 30,936 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 0.63 (30936 hom., cov: 32)
• Consequence: ENSG00000298549 ENST00000756364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836
• Publications: 10 publications found

Genes affected

ENSG00000298549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756364.1. 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
	ENSG00000298549	ENST00000756364.1		n.129-42457A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96440 AN: 151888 Hom.: 30919 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.635 AC: 96507 AN: 152006 Hom.: 30936 Cov.: 32 AF XY: 0.636 AC XY: 47252 AN XY: 74270

African (AFR) AF: 0.533 AC: 22076 AN: 41430

American (AMR) AF: 0.604 AC: 9222 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2116 AN: 3472

East Asian (EAS) AF: 0.776 AC: 4021 AN: 5182

South Asian (SAS) AF: 0.638 AC: 3070 AN: 4812

European-Finnish (FIN) AF: 0.641 AC: 6767 AN: 10550

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.691 AC: 46963 AN: 67974

Other (OTH) AF: 0.655 AC: 1382 AN: 2110

Alfa AF: 0.650 Hom.: 14600

Bravo AF: 0.628

Asia WGS AF: 0.660 AC: 2293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.46
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs754387; hg19: chr6-88878859;