rs6457580

Variant names:

• chr6-32425364-G-T
• rs6457580
• ENST00000766247.1:n.283-8728G>T

Variant summary

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

The ENST00000766248.1(ENSG00000299769):​n.287-4G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 152,314 control chromosomes in the GnomAD database, including 123 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 0.024 (123 hom., cov: 34)
• Consequence: ENSG00000299769 ENST00000766248.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 10 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766248.1. 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
	ENSG00000299769	ENST00000766247.1		n.283-8728G>T		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.287-4G>T		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0239 AC: 3641 AN: 152196 Hom.: 125 Cov.: 34

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.00962

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.0749

Gnomad SAS AF: 0.0103

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00285

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0239 AC: 3641 AN: 152314 Hom.: 123 Cov.: 34 AF XY: 0.0240 AC XY: 1787 AN XY: 74494

African (AFR) AF: 0.0673 AC: 2797 AN: 41564

American (AMR) AF: 0.00961 AC: 147 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3470

East Asian (EAS) AF: 0.0749 AC: 388 AN: 5180

South Asian (SAS) AF: 0.00973 AC: 47 AN: 4828

European-Finnish (FIN) AF: 0.000565 AC: 6 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00284 AC: 193 AN: 68032

Other (OTH) AF: 0.0241 AC: 51 AN: 2112

Alfa AF: 0.0159 Hom.: 109

Bravo AF: 0.0271

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.71
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs6457580; hg19: chr6-32393141;