6-54536491-T-C

Variant names:

• chr6-54536491-T-C
• rs659446
• ENST00000763589.1:n.449-14956A>G

Variant summary

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

The ENST00000763589.1(ENSG00000299445):​n.449-14956A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,832 control chromosomes in the GnomAD database, including 5,402 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 0.23 (5402 hom., cov: 31)
• Consequence: ENSG00000299445 ENST00000763589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 3 publications found

Genes affected

ENSG00000299445 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763589.1. 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
	ENSG00000299445	ENST00000763589.1		n.449-14956A>G		intron	N/A
	ENSG00000299445	ENST00000763590.1		n.330-16334A>G		intron	N/A
	ENSG00000299445	ENST00000763594.1		n.128-14956A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35144 AN: 151714 Hom.: 5393 Cov.: 31

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.232 AC: 35154 AN: 151832 Hom.: 5402 Cov.: 31 AF XY: 0.240 AC XY: 17774 AN XY: 74176

African (AFR) AF: 0.0597 AC: 2476 AN: 41494

American (AMR) AF: 0.417 AC: 6341 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 899 AN: 3466

East Asian (EAS) AF: 0.550 AC: 2819 AN: 5126

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4822

European-Finnish (FIN) AF: 0.312 AC: 3289 AN: 10534

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17292 AN: 67854

Other (OTH) AF: 0.273 AC: 577 AN: 2112

Alfa AF: 0.242 Hom.: 958

Bravo AF: 0.237

Asia WGS AF: 0.334 AC: 1162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.52
PhyloP100		0.046

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: rs659446;

hg19: chr6-54401289;